Merge branch 'master' into dev/bioimaging

bgruening · Jan 7, 2025 · 93892d6 · 93892d6
2 parents c51e7b0 + 373c81f
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diff --git a/tools/augustus/.shed.yml → deprecated/tools/augustus/.shed.yml b/tools/augustus/.shed.yml → deprecated/tools/augustus/.shed.yml
diff --git a/tools/augustus/augustus.xml → deprecated/tools/augustus/augustus.xml b/tools/augustus/augustus.xml → deprecated/tools/augustus/augustus.xml
diff --git a/tools/augustus/extract_features.py → ...ecated/tools/augustus/extract_features.py b/tools/augustus/extract_features.py → ...ecated/tools/augustus/extract_features.py
diff --git a/tools/augustus/readme.rst → deprecated/tools/augustus/readme.rst b/tools/augustus/readme.rst → deprecated/tools/augustus/readme.rst
diff --git a/...ugustus/test-data/arabidopsis_augustus.fa → ...ugustus/test-data/arabidopsis_augustus.fa b/...ugustus/test-data/arabidopsis_augustus.fa → ...ugustus/test-data/arabidopsis_augustus.fa
diff --git a/tools/augustus/test-data/human_augustus.fa → ...ools/augustus/test-data/human_augustus.fa b/tools/augustus/test-data/human_augustus.fa → ...ools/augustus/test-data/human_augustus.fa
diff --git a/...ein_codingseq_introns_cds_codingseq.fasta → ...ein_codingseq_introns_cds_codingseq.fasta b/...ein_codingseq_introns_cds_codingseq.fasta → ...ein_codingseq_introns_cds_codingseq.fasta
diff --git a/...us_protein_codingseq_introns_cds_main.gtf → ...us_protein_codingseq_introns_cds_main.gtf b/...us_protein_codingseq_introns_cds_main.gtf → ...us_protein_codingseq_introns_cds_main.gtf
diff --git a/...otein_codingseq_introns_cds_protein.fasta → ...otein_codingseq_introns_cds_protein.fasta b/...otein_codingseq_introns_cds_protein.fasta → ...otein_codingseq_introns_cds_protein.fasta
diff --git a/...ustus/test-data/human_augustus_utr-on.gff → ...ustus/test-data/human_augustus_utr-on.gff b/...ustus/test-data/human_augustus_utr-on.gff → ...ustus/test-data/human_augustus_utr-on.gff
diff --git a/...ustus/test-data/human_augustus_utr-on.gtf → ...ustus/test-data/human_augustus_utr-on.gtf b/...ustus/test-data/human_augustus_utr-on.gtf → ...ustus/test-data/human_augustus_utr-on.gtf
diff --git a/tools/augustus/tool_dependencies.xml → ...ated/tools/augustus/tool_dependencies.xml b/tools/augustus/tool_dependencies.xml → ...ated/tools/augustus/tool_dependencies.xml
diff --git a/tools/blobtoolkit/blobtoolkit.xml b/tools/blobtoolkit/blobtoolkit.xml
@@ -477,7 +477,7 @@
     
 **NCBI taxdump directory**
 
-The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file **new_taxdump.tar.gz** can be downloaded from the taxonomy directory on the `FTP site <ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_. 
+The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file **new_taxdump.tar.gz** can be downloaded from the taxonomy directory on the `FTP site <https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_. 
     
     ]]></help>
     <expand macro="citations"/>

diff --git a/tools/cellprofiler_v4/macros.xml b/tools/cellprofiler_v4/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">4.2.7</token>
+    <token name="@TOOL_VERSION@">4.2.8</token>
     <token name="@PY_VERSION@">3.8</token>
     <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
     <token name="@SPACES@">"    "</token>

diff --git 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>
@@ -13,10 +13,18 @@
         <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 == '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 $report_format.report_format_select == 'txt_columns'
+            -y
+        #end if
+        ## If the compared input files differ the diff command returns exit-code 1
+        '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
+        #if $report_format.report_format_select == 'html'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-                -e 's/@@outputformat@@/'$output_format'/g'
+                -e 's/@@outputformat@@/'$report_format.output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                 '$__tool_directory__/template.html' > '$html_file'
         #end if
@@ -25,33 +33,50 @@
     <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">
+                <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 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>
+        </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>generate_report is True</filter>
+            <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="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"/>
                 </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="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 +88,9 @@
         <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 +100,10 @@
         <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 +114,10 @@
         <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"/>
@@ -95,9 +126,12 @@
             </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"/>
-            <param name="generate_report" value="true"/>
+            <param name="input1" value="file3.txt"/>
+            <param name="input2" value="file3.txt"/>
+            <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"/>
@@ -169,4 +203,4 @@ An **optional** *HTML report* with a friendlier visual representation of the dif
             }
         </citation>
     </citations>
-</tool>
+</tool>
diff --git a/tools/diff/test-data/file 3.txt → tools/diff/test-data/file3.txt b/tools/diff/test-data/file 3.txt → tools/diff/test-data/file3.txt
diff --git a/tools/diff/test-data/output_test4.txt b/tools/diff/test-data/output_test4.txt
@@ -0,0 +1,2 @@
+a								a
+							      >	b
diff --git a/tools/flux/flux.py b/tools/flux/flux.py
@@ -12,6 +12,7 @@
         prompt = f.read().strip()
 elif prompt_type == "text":
     prompt = sys.argv[3]
+print(f"Creating image from prompt: {prompt}")
 
 if "dev" in model_path:
     num_inference_steps = 20

diff --git a/tools/flux/flux.xml b/tools/flux/flux.xml
@@ -2,30 +2,21 @@
     <description>text-to-image model</description>
     <macros>
         <token name="@TOOL_VERSION@">2024</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">4</token>
     </macros>
     <requirements>
-        <requirement type="package" version="3.12">python</requirement>
-        <requirement type="package" version="2.4.1">pytorch</requirement>
-        <requirement type="package" version="0.19.1">torchvision</requirement>
-        <requirement type="package" version="12.4">pytorch-cuda</requirement>
-        <requirement type="package" version="0.30.2">diffusers</requirement>
-        <requirement type="package" version="4.44.2">transformers</requirement>
-        <requirement type="package" version="0.34.0">accelerate</requirement>
-        <requirement type="package" version="0.2.0">sentencepiece</requirement>
-        <requirement type="package" version="4.25.3">protobuf</requirement>
-        <requirement type="package" version="0.24.6">huggingface_hub</requirement>
+        <container type="docker">quay.io/galaxy/black_forest_labs_flux:2024-0</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/flux.py'
+python3 '$__tool_directory__/flux.py'
 '$flux_models.fields.path'
 '$input_type_selector'
 '$prompt'
     ]]></command>
     <configfiles>
     </configfiles>
     <inputs>
-        <param name="flux_models" label="Model data" type="select" help="contact the administrator of this Galaxy instance if you miss model data">
+        <param name="flux_models" label="Model data" type="select" help="Contact the administrator of our Galaxy instance if you miss model data">
             <options from_data_table="huggingface">
                 <filter type="static_value" column="4" value="flux"/>
                 <filter type="static_value" column="5" value="1"/>
@@ -48,7 +39,7 @@ python '$__tool_directory__/flux.py'
         </conditional>
     </inputs>
     <outputs>
-        <data name="output" format="png" label="${tool.name} on ${on_string}" from_work_dir="./output.png"/>
+        <data name="output" format="png" label="${tool.name} on ${on_string if $input_type_selector=='file' else 'text prompt'}" from_work_dir="./output.png"/>
     </outputs>
     <tests>
         <test expect_exit_code="1" expect_failure="true">

diff --git a/tools/flye/flye.xml b/tools/flye/flye.xml
@@ -105,7 +105,7 @@
     <outputs>
         <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
         <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
-        <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
+        <data name="assembly_gfa" format="gfa1" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
         <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
         <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
             <filter>generate_log</filter>
@@ -115,12 +115,14 @@
         <!--Test 01: pacbio-raw-->
         <test expect_num_outputs="5">
             <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
-            <param name="mode" value="--pacbio-raw"/>
+            <conditional name="mode_conditional">
+                <param name="mode" value="--pacbio-raw"/>
+            </conditional>
             <param name="iterations" value="0"/>
             <param name="generate_log" value="true"/>
             <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
-            <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>
+            <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa1" compare="diff" lines_diff="10"/>
             <output name="consensus" ftype="fasta">
                 <assert_contents>
                     <has_line line=">contig_1"/>
@@ -131,7 +133,9 @@
         <!--Test 02: nano raw-->
         <test expect_num_outputs="4">
             <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
-            <param name="mode" value="--nano-raw"/>
+            <conditional name="mode_conditional">
+                <param name="mode" value="--nano-raw"/>
+            </conditional>
             <param name="iterations" value="0"/>
             <output name="assembly_info" ftype="tabular">
                 <assert_contents>
@@ -143,7 +147,7 @@
                     <has_size value="803" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="35047" delta="100"/>
                </assert_contents>
@@ -162,7 +166,7 @@
             </conditional>
             <conditional name="asm">
                 <param name="asm_select" value="true" />
-                <param name="asm" value="30"/>
+                <param name="asm_coverage" value="30"/>
                 <param name="genome_size" value="3980000"/>
             </conditional>
             <output name="assembly_info" ftype="tabular">
@@ -175,7 +179,7 @@
                     <has_size value="1840" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="420752" delta="100"/>
                </assert_contents>
@@ -203,7 +207,7 @@
                     <has_size value="367" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="418729" delta="100"/>
                </assert_contents>
@@ -231,7 +235,7 @@
                     <has_size value="1248" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="419414" delta="1000"/>
                </assert_contents>
@@ -260,7 +264,7 @@
                     <has_size value="1248" delta="500"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="420254" delta="2000"/>
                </assert_contents>
@@ -276,10 +280,9 @@
             <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
             <conditional name="mode_conditional">
                 <param name="mode" value="--pacbio-corr"/>
-                <param name="hifi_error" value="0.21"/>
             </conditional>
             <param name="min_overlap" value="1000"/>
-            <param name="keep-haplotypes" value="true"/>
+            <param name="keep_haplotypes" value="true"/>
             <output name="assembly_info" ftype="tabular">
                 <assert_contents>
                     <has_size value="286" delta="200"/>
@@ -290,7 +293,7 @@
                     <has_size value="1273" delta="500"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="420254" delta="3000"/>
                </assert_contents>
@@ -304,7 +307,9 @@
         <!--Test 08: scaffolding mode-->
         <test expect_num_outputs="4">
             <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
-            <param name="mode" value="--nano-hq"/>
+            <conditional name="mode_conditional">
+                <param name="mode" value="--nano-hq"/>
+            </conditional>
             <param name="min_overlap" value="1000"/>
             <param name="scaffold" value="true"/>
             <output name="assembly_info" ftype="tabular">
@@ -317,7 +322,7 @@
                     <has_size value="1248" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="419414" delta="2000"/>
                </assert_contents>
@@ -331,7 +336,9 @@
         <!--Test 09: test not-alt-contigs parameter w-->
         <test expect_num_outputs="4">
             <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
-            <param name="mode" value="--nano-raw"/>
+            <conditional name="mode_conditional">
+                <param name="mode" value="--nano-raw"/>
+            </conditional>
             <param name="iterations" value="0"/>
             <param name="no_alt_contigs" value="true"/>
             <output name="assembly_info" ftype="tabular">
@@ -344,7 +351,7 @@
                     <has_size value="217" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="gfa">
+            <output name="assembly_gfa" ftype="gfa1">
                 <assert_contents>
                     <has_size value="5110" delta="100"/>
                </assert_contents>

diff --git a/tools/flye/macros.xml b/tools/flye/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.9.5</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">flye</requirement>