From db3e99263e79e6b38a47cfec12822d358bf0a6df Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 Dec 2024 11:32:11 +0100
Subject: [PATCH 01/11] add new -y parameter, bump version, adopt tests, WIP

---
 tools/diff/diff.xml | 64 +++++++++++++++++++++++++++++++++------------
 1 file changed, 47 insertions(+), 17 deletions(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index b3070c6903..7cd685d4ee 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -1,7 +1,7 @@
-<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.7</token>
+        <token name="@TOOL_VERSION@">3.10</token>
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <requirements>
@@ -13,8 +13,15 @@
         <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
     </stdio>
     <command><![CDATA[
-        diff -u '$input1' '$input2' > '$diff_file';
-        #if $generate_report:
+        diff
+        #if $report_format.report_format_select in ['txt_lines', 'html']:
+            ## the -u option is needed to convert the output later to HTML
+            -u
+        #else if $report_format.report_format_select == 'txt_columns':
+            -y
+        #end if
+        '$input1' '$input2' > '$diff_file' &&
+        #if $report_format.report_format_select == 'html':
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
                 -e 's/@@outputformat@@/'$output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
@@ -25,11 +32,21 @@
     <inputs>
         <param name="input1" type="data" format="txt" label="First input file"/>
         <param name="input2" type="data" format="txt" label="Second input file"/>
-        <param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/>
-        <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
-            <option value="side-by-side">Side by side</option>
-            <option value="line-by-line">Line by line</option>
-        </param>
+        <conditional name="report_format">
+            <param name="report_format_select" type="select" label="Choose a report format">
+                <option value="txt_lines">Text file, line-by-line (-u)</option>
+                <option value="txt_columns">Text file, side-by-side (-y)</option>
+                <option value="html">Generates an HTML report to visualize the differences</option>
+            </param>
+            <when value="txt_lines"/>
+            <when value="txt_columns"/>
+            <when value="html">
+                <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
+                    <option value="side-by-side">Side by side</option>
+                    <option value="line-by-line">Line by line</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
@@ -41,7 +58,9 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file1.txt"/>
-            <param name="generate_report" value="false"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
@@ -51,7 +70,9 @@
         <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="false"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="5"/>
@@ -63,7 +84,9 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -73,8 +96,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
-            <param name="output_format" value="side-by-side"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -85,8 +110,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
-            <param name="output_format" value="line-by-line"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="line-by-line"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -97,7 +124,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file 3.txt"/>
             <param name="input2" value="file 3.txt"/>
-            <param name="generate_report" value="true"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>

From deb7f1c9fcb76547dc31d1031a3841d097a505ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Mon, 2 Dec 2024 12:10:39 +0100
Subject: [PATCH 02/11] Update diff.xml

---
 tools/diff/diff.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 7cd685d4ee..b4da2d4061 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -20,8 +20,9 @@
         #else if $report_format.report_format_select == 'txt_columns':
             -y
         #end if
-        '$input1' '$input2' > '$diff_file' &&
+        '$input1' '$input2' > '$diff_file'
         #if $report_format.report_format_select == 'html':
+            &&
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
                 -e 's/@@outputformat@@/'$output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'

From 66f1622c4660b595b9837cc8ff546e2bb705ce50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Mon, 2 Dec 2024 12:45:43 +0100
Subject: [PATCH 03/11] Update diff.xml

---
 tools/diff/diff.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index b4da2d4061..eefba264a9 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -52,7 +52,7 @@
     <outputs>
         <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
         <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
-            <filter>generate_report is True</filter>
+            <filter>report_format['report_format_select'] == 'html'</filter>
         </data>
     </outputs>
     <tests>

From 667a7acf3a1cee36b8ce5718d7893bd8bb9f59ce Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 Dec 2024 13:01:44 +0100
Subject: [PATCH 04/11] add unified option with integer

---
 tools/diff/diff.xml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index eefba264a9..c6972cf5a7 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -16,7 +16,7 @@
         diff
         #if $report_format.report_format_select in ['txt_lines', 'html']:
             ## the -u option is needed to convert the output later to HTML
-            -u
+            --unified $report_format.unified
         #else if $report_format.report_format_select == 'txt_columns':
             -y
         #end if
@@ -39,7 +39,9 @@
                 <option value="txt_columns">Text file, side-by-side (-y)</option>
                 <option value="html">Generates an HTML report to visualize the differences</option>
             </param>
-            <when value="txt_lines"/>
+            <when value="txt_lines">
+                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
+            </when>
             <when value="txt_columns"/>
             <when value="html">
                 <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">

From c4f6fedd2ee7ab27dc51f614fc484682c74c880a Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 Dec 2024 13:04:49 +0100
Subject: [PATCH 05/11] fix another missing template

---
 tools/diff/diff.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index c6972cf5a7..892458b87d 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -17,14 +17,14 @@
         #if $report_format.report_format_select in ['txt_lines', 'html']:
             ## the -u option is needed to convert the output later to HTML
             --unified $report_format.unified
-        #else if $report_format.report_format_select == 'txt_columns':
+        #else if $report_format.report_format_select == 'txt_columns':  
             -y
         #end if
         '$input1' '$input2' > '$diff_file'
         #if $report_format.report_format_select == 'html':
             &&
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-                -e 's/@@outputformat@@/'$output_format'/g'
+                -e 's/@@outputformat@@/'$report_format_select.output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                 '$__tool_directory__/template.html' > '$html_file'
         #end if

From 6cc4955b91a899ce90fe088a88607490456290d1 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Wed, 4 Dec 2024 15:28:40 +0100
Subject: [PATCH 06/11] adjust command and input/output sections and add tests

---
 tools/diff/diff.xml                           | 121 ++++++++++--------
 .../diff/test-data/{file 3.txt => file3.txt}  |   0
 tools/diff/test-data/output_test4.txt         |   2 +
 3 files changed, 73 insertions(+), 50 deletions(-)
 rename tools/diff/test-data/{file 3.txt => file3.txt} (100%)
 create mode 100644 tools/diff/test-data/output_test4.txt

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 892458b87d..84612485e5 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -1,4 +1,4 @@
-<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
+<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
         <token name="@TOOL_VERSION@">3.10</token>
@@ -14,17 +14,20 @@
     </stdio>
     <command><![CDATA[
         diff
-        #if $report_format.report_format_select in ['txt_lines', 'html']:
-            ## the -u option is needed to convert the output later to HTML
-            --unified $report_format.unified
-        #else if $report_format.report_format_select == 'txt_columns':  
-            -y
+        #if $HTML_report.HTML_report_select == 'yes'
+            ## the --unified option is needed to convert the output later to HTML
+            --unified=$HTML_report.unified
+        #else 
+            #if $HTML_report.output_format_raw.output_format_raw_select == 'txt_lines'
+                --unified=$HTML_report.output_format_raw.unified
+            #elif $HTML_report.output_format_raw.output_format_raw_select == 'txt_columns'
+                -y
+            #end if
         #end if
-        '$input1' '$input2' > '$diff_file'
-        #if $report_format.report_format_select == 'html':
-            &&
+        '$input1' '$input2' > '$diff_file';
+        #if $HTML_report.HTML_report_select == 'yes'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-                -e 's/@@outputformat@@/'$report_format_select.output_format'/g'
+                -e 's/@@outputformat@@/'$HTML_report.output_format_html_select'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                 '$__tool_directory__/template.html' > '$html_file'
         #end if
@@ -33,37 +36,45 @@
     <inputs>
         <param name="input1" type="data" format="txt" label="First input file"/>
         <param name="input2" type="data" format="txt" label="Second input file"/>
-        <conditional name="report_format">
-            <param name="report_format_select" type="select" label="Choose a report format">
-                <option value="txt_lines">Text file, line-by-line (-u)</option>
-                <option value="txt_columns">Text file, side-by-side (-y)</option>
-                <option value="html">Generates an HTML report to visualize the differences</option>
+        <conditional name="HTML_report">
+            <param name="HTML_report_select" type="select" label="Generate an HTML report?" help="Generates an HTML report to visualize the differences">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
             </param>
-            <when value="txt_lines">
+            <when value="yes">
                 <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
-            </when>
-            <when value="txt_columns"/>
-            <when value="html">
-                <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
+                <param name="output_format_html_select" type="select" label="Choose HTML report output format" help="Displays the differences in the HTML report using the selected format. Either line by line or side by side.">
                     <option value="side-by-side">Side by side</option>
                     <option value="line-by-line">Line by line</option>
                 </param>
             </when>
+            <when value="no">
+                <conditional name="output_format_raw">
+                    <param name="output_format_raw_select" type="select" label="Choose report output format" help="Displays the differences in the raw output using the selected format. Either line by line or side by side.">
+                        <option value="">None</option>
+                        <option value="txt_lines">Text file, line-by-line (-u)</option>
+                        <option value="txt_columns">Text file, side-by-side (-y)</option>
+                    </param>
+                    <when value="txt_lines">
+                        <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
+                    </when>
+                    <when value="txt_columns" />
+                    <when value="" />
+                </conditional>
+            </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
-        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
-            <filter>report_format['report_format_select'] == 'html'</filter>
+        <data format="txt" name="diff_file" label="${tool.name} on ${on_string}: Raw Output"/>
+        <data format="html" name="html_file" label="${tool.name} on ${on_string}: Html Report">
+            <filter>HTML_report['HTML_report_select'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file1.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="txt_lines"/>
-            </conditional>
+            <param name="HTML_report_select" value="no"/>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
@@ -73,23 +84,40 @@
         <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="txt_lines"/>
-            </conditional>
+            <param name="HTML_report_select" value="no"/>
+            <output name="diff_file">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_line line="1a2"/>
+                    <has_line line="> b"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
+            <param name="input1" value="file1.txt"/>
+            <param name="input2" value="file2.txt"/>
+            <param name="HTML_report_select" value="no"/>
+            <param name="output_format_raw_select" value="txt_lines"/>
+            <param name="unified" value="4"/>
             <output name="diff_file">
                 <assert_contents>
-                    <has_n_lines n="5"/>
-                    <has_line line=" a"/>
-                    <has_line line="+b"/>
+                    <has_n_lines n="5" />
+                    <has_line line=" a" />
+                    <has_line line="+b" />
                 </assert_contents>
             </output>
         </test>
+        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
+            <param name="input1" value="file1.txt"/>
+            <param name="input2" value="file2.txt"/>
+            <param name="HTML_report_select" value="no"/>
+            <param name="output_format_raw_select" value="txt_columns"/>
+            <output name="diff_file" file="output_test4.txt" />
+        </test>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="html"/>
-            </conditional>
+            <param name="HTML_report_select" value="yes"/>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -99,10 +127,8 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="html"/>
-                <param name="output_format" value="side-by-side"/>
-            </conditional>
+            <param name="HTML_report_select" value="yes"/>
+            <param name="output_format_html_select" value="side-by-side"/>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -113,10 +139,8 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="html"/>
-                <param name="output_format" value="line-by-line"/>
-            </conditional>
+            <param name="HTML_report_select" value="yes"/>
+            <param name="output_format_html_select" value="line-by-line"/>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -125,12 +149,9 @@
             </output>
         </test>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
-            <param name="input1" value="file 3.txt"/>
-            <param name="input2" value="file 3.txt"/>
-            <conditional name="report_format">
-                <param name="report_format_select" value="html"/>
-                <param name="output_format" value="side-by-side"/>
-            </conditional>
+            <param name="input1" value="file3.txt"/>
+            <param name="input2" value="file3.txt"/>
+            <param name="HTML_report_select" value="yes"/>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
@@ -202,4 +223,4 @@ An **optional** *HTML report* with a friendlier visual representation of the dif
             }
         </citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file
diff --git a/tools/diff/test-data/file 3.txt b/tools/diff/test-data/file3.txt
similarity index 100%
rename from tools/diff/test-data/file 3.txt
rename to tools/diff/test-data/file3.txt
diff --git a/tools/diff/test-data/output_test4.txt b/tools/diff/test-data/output_test4.txt
new file mode 100644
index 0000000000..db4ccf3cd8
--- /dev/null
+++ b/tools/diff/test-data/output_test4.txt
@@ -0,0 +1,2 @@
+a								a
+							      >	b

From 9ce769ee73ae288fe74b1dbbf98595914c3b094d Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Wed, 4 Dec 2024 15:44:17 +0100
Subject: [PATCH 07/11] increment version suffix

---
 tools/diff/diff.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 84612485e5..26e26fcd09 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -2,7 +2,7 @@
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
         <token name="@TOOL_VERSION@">3.10</token>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>

From 174ef20cfa9899fbb2d82e7868f33658a58b9666 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Wed, 4 Dec 2024 15:49:32 +0100
Subject: [PATCH 08/11] re-add profile

---
 tools/diff/diff.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 26e26fcd09..0cd9fb8378 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -1,4 +1,4 @@
-<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
         <token name="@TOOL_VERSION@">3.10</token>

From a78055534e3bcb01bc62a33b9ae61164c39edc06 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Mon, 9 Dec 2024 14:01:09 +0100
Subject: [PATCH 09/11] handle diff exit-code 1

---
 tools/diff/diff.xml | 117 ++++++++++++++++++--------------------------
 1 file changed, 48 insertions(+), 69 deletions(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 0cd9fb8378..69e9893278 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -2,7 +2,7 @@
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
         <token name="@TOOL_VERSION@">3.10</token>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>
@@ -14,20 +14,16 @@
     </stdio>
     <command><![CDATA[
         diff
-        #if $HTML_report.HTML_report_select == 'yes'
-            ## the --unified option is needed to convert the output later to HTML
-            --unified=$HTML_report.unified
-        #else 
-            #if $HTML_report.output_format_raw.output_format_raw_select == 'txt_lines'
-                --unified=$HTML_report.output_format_raw.unified
-            #elif $HTML_report.output_format_raw.output_format_raw_select == 'txt_columns'
-                -y
-            #end if
+        #if $report_format.report_format_select == 'txt_lines' or $report_format.report_format_select == 'html'
+            ## the -u option is needed to convert the output later to HTML
+            --unified=$report_format.unified
+        #else if $report_format.report_format_select == 'txt_columns'
+            -y
         #end if
-        '$input1' '$input2' > '$diff_file';
-        #if $HTML_report.HTML_report_select == 'yes'
+        '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
+        #if $report_format.report_format_select == 'html'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-                -e 's/@@outputformat@@/'$HTML_report.output_format_html_select'/g'
+                -e 's/@@outputformat@@/'$report_format.output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                 '$__tool_directory__/template.html' > '$html_file'
         #end if
@@ -36,88 +32,64 @@
     <inputs>
         <param name="input1" type="data" format="txt" label="First input file"/>
         <param name="input2" type="data" format="txt" label="Second input file"/>
-        <conditional name="HTML_report">
-            <param name="HTML_report_select" type="select" label="Generate an HTML report?" help="Generates an HTML report to visualize the differences">
-                <option value="yes">Yes</option>
-                <option value="no">No</option>
+        <conditional name="report_format">
+            <param name="report_format_select" type="select" label="Choose a report format">
+                <option value="txt_lines">Text file, line-by-line (-u)</option>
+                <option value="txt_columns">Text file, side-by-side (-y)</option>
+                <option value="html">Generates an HTML report to visualize the differences</option>
             </param>
-            <when value="yes">
+            <when value="txt_lines">
                 <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
-                <param name="output_format_html_select" type="select" label="Choose HTML report output format" help="Displays the differences in the HTML report using the selected format. Either line by line or side by side.">
+            </when>
+            <when value="txt_columns"/>
+            <when value="html">
+                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
+                <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
                     <option value="side-by-side">Side by side</option>
                     <option value="line-by-line">Line by line</option>
                 </param>
             </when>
-            <when value="no">
-                <conditional name="output_format_raw">
-                    <param name="output_format_raw_select" type="select" label="Choose report output format" help="Displays the differences in the raw output using the selected format. Either line by line or side by side.">
-                        <option value="">None</option>
-                        <option value="txt_lines">Text file, line-by-line (-u)</option>
-                        <option value="txt_columns">Text file, side-by-side (-y)</option>
-                    </param>
-                    <when value="txt_lines">
-                        <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
-                    </when>
-                    <when value="txt_columns" />
-                    <when value="" />
-                </conditional>
-            </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="diff_file" label="${tool.name} on ${on_string}: Raw Output"/>
-        <data format="html" name="html_file" label="${tool.name} on ${on_string}: Html Report">
-            <filter>HTML_report['HTML_report_select'] == 'yes'</filter>
+        <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
+        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
+            <filter>report_format['report_format_select'] == 'html'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file1.txt"/>
-            <param name="HTML_report_select" value="no"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
-            <param name="input1" value="file1.txt"/>
-            <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="no"/>
-            <output name="diff_file">
-                <assert_contents>
-                    <has_n_lines n="2"/>
-                    <has_line line="1a2"/>
-                    <has_line line="> b"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
+        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="no"/>
-            <param name="output_format_raw_select" value="txt_lines"/>
-            <param name="unified" value="4"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
-                    <has_n_lines n="5" />
-                    <has_line line=" a" />
-                    <has_line line="+b" />
+                    <has_n_lines n="5"/>
+                    <has_line line=" a"/>
+                    <has_line line="+b"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
-            <param name="input1" value="file1.txt"/>
-            <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="no"/>
-            <param name="output_format_raw_select" value="txt_columns"/>
-            <output name="diff_file" file="output_test4.txt" />
-        </test>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="yes"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -127,8 +99,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="yes"/>
-            <param name="output_format_html_select" value="side-by-side"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -139,8 +113,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="HTML_report_select" value="yes"/>
-            <param name="output_format_html_select" value="line-by-line"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="line-by-line"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -151,7 +127,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file3.txt"/>
             <param name="input2" value="file3.txt"/>
-            <param name="HTML_report_select" value="yes"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>

From fd72412a843a00b7d505ec9624c581249c590d37 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Mon, 9 Dec 2024 15:08:03 +0100
Subject: [PATCH 10/11] add a comment

---
 tools/diff/diff.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 69e9893278..3946888426 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -20,6 +20,7 @@
         #else if $report_format.report_format_select == 'txt_columns'
             -y
         #end if
+        ## If the compared input files differ the diff command return exit-code 1
         '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
         #if $report_format.report_format_select == 'html'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'

From 3c61e1cb3c09e230c6587eb82c6649fc8e2c5347 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Mon, 9 Dec 2024 15:10:39 +0100
Subject: [PATCH 11/11] typo

---
 tools/diff/diff.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/diff/diff.xml b/tools/diff/diff.xml
index 3946888426..3ae9bb00b9 100644
--- a/tools/diff/diff.xml
+++ b/tools/diff/diff.xml
@@ -20,7 +20,7 @@
         #else if $report_format.report_format_select == 'txt_columns'
             -y
         #end if
-        ## If the compared input files differ the diff command return exit-code 1
+        ## If the compared input files differ the diff command returns exit-code 1
         '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
         #if $report_format.report_format_select == 'html'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'