| Previous changeset 2:add230dddd52 (2022-09-26) Next changeset 4:3d61a698e5e1 (2023-03-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078 |
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modified:
arriba.xml macros.xml |
| b |
| diff -r add230dddd52 -r f6b8b38636a4 arriba.xml --- a/arriba.xml Mon Sep 26 09:32:30 2022 +0000 +++ b/arriba.xml Tue Dec 06 10:38:51 2022 +0000 |
| [ |
| @@ -154,7 +154,7 @@ $options.duplicate_marking $options.fill_discarded_columns $options.fill_the_gaps -#if str($visualization.do_viz) == "yes" +#if $output_fusion_bams or str($visualization.do_viz) == "yes" && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #end if @@ -441,16 +441,13 @@ <discover_datasets pattern="(?P<name>fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/> <filter>output_fusion_bams == True</filter> </collection> - <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> - <filter>input_params['input_source'] == "use_fastq"</filter> - </data> <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> <filter>visualization['do_viz'] == "yes"</filter> </data> </outputs> <tests> <!-- Test 1 - From exisitng BAM --> - <test> + <test expect_num_outputs="3"> <param name="input" ftype="sam" value="Aligned.out.sam"/> <conditional name="genome"> <param name="genome_source" value="history"/> @@ -472,7 +469,7 @@ </output> </test> <!-- Test 2 - From exisitng BAM with protein_domains and visualization --> - <test> + <test expect_num_outputs="4"> <param name="input" ftype="sam" value="Aligned.out.sam"/> <conditional name="genome"> <param name="genome_source" value="history"/> |
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| diff -r add230dddd52 -r f6b8b38636a4 macros.xml --- a/macros.xml Mon Sep 26 09:32:30 2022 +0000 +++ b/macros.xml Tue Dec 06 10:38:51 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.3.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> |