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Diff add -y parameter #1555

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merged 11 commits into from
Dec 9, 2024
Merged

Diff add -y parameter #1555

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db3e992
add new -y parameter, bump version, adopt tests, WIP
bgruening Dec 2, 2024
deb7f1c
Update diff.xml
bgruening Dec 2, 2024
66f1622
Update diff.xml
bgruening Dec 2, 2024
667a7ac
add unified option with integer
bgruening Dec 2, 2024
c4f6fed
fix another missing template
bgruening Dec 2, 2024
6cc4955
adjust command and input/output sections and add tests
RZ9082 Dec 4, 2024
9ce769e
increment version suffix
RZ9082 Dec 4, 2024
174ef20
re-add profile
RZ9082 Dec 4, 2024
a780555
handle diff exit-code 1
RZ9082 Dec 9, 2024
fd72412
add a comment
RZ9082 Dec 9, 2024
3c61e1c
typo
RZ9082 Dec 9, 2024
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121 changes: 71 additions & 50 deletions tools/diff/diff.xml
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Original file line number Diff line number Diff line change
@@ -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>
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<macros>
<token name="@TOOL_VERSION@">3.10</token>
Expand All @@ -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
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -202,4 +223,4 @@ An **optional** *HTML report* with a friendlier visual representation of the dif
}
</citation>
</citations>
</tool>
</tool>
0 tools/diff/test-data/file 3.txt → tools/diff/test-data/file3.txt
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2 changes: 2 additions & 0 deletions tools/diff/test-data/output_test4.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
a a
> b
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