| Previous changeset 2:ec07e22c41f8 (2024-04-22) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 |
|
modified:
batch.xml macros.xml |
| b |
| diff -r ec07e22c41f8 -r 97d2b6742760 batch.xml --- a/batch.xml Mon Apr 22 17:44:06 2024 +0000 +++ b/batch.xml Fri Dec 13 23:59:44 2024 +0000 |
| b |
| @@ -147,16 +147,20 @@ </outputs> <tests> <test expect_num_outputs="13"> - <conditional name="reference_source"> - <param name="ref_selector" value="history"/> - <param name="fasta" ftype="fasta" value="genome.fasta" /> + <conditional name="CNV_reference"> + <conditional name="reference_source"> + <param name="ref_selector" value="history"/> + <param name="fasta" ftype="fasta" value="genome.fasta" /> + </conditional> + <param name="CNV_reference_availabel" value="no" /> + <param name="input_sample_file" ftype="bam" value="tumor.bam" /> + <param name="normal" ftype="bam" value="normal.bam" /> + <param name="targets" ftype="bed" value="capture.bed" /> </conditional> - <param name="CNV_reference_availabel" value="no" /> - <param name="input_sample_file" ftype="bam" value="tumor.bam" /> - <param name="normal" ftype="bam" value="normal.bam" /> - <param name="targets" ftype="bed" value="capture.bed" /> - <param name="scatter" value="1"/> - <param name="diagram" value="1"/> + <section name="output_section"> + <param name="scatter" value="1"/> + <param name="diagram" value="1"/> + </section> <output name="out_sample_bintest" file="tumor.bintest.cns" /> <output name="out_sample_antitargetcoverage"> <assert_contents><has_text text="chromosome"/></assert_contents> @@ -190,16 +194,20 @@ </output> </test> <test expect_num_outputs="13"> - <conditional name="reference_source"> - <param name="ref_selector" value="cached"/> - <param name="fasta" value="test_buildid"/> + <conditional name="CNV_reference"> + <conditional name="reference_source"> + <param name="ref_selector" value="cached"/> + <param name="fasta" value="test_buildid"/> + </conditional> + <param name="CNV_reference_availabel" value="no" /> + <param name="input_sample_file" ftype="bam" value="tumor.bam" /> + <param name="normal" ftype="bam" value="normal.bam" /> + <param name="targets" ftype="bed" value="capture.bed" /> </conditional> - <param name="CNV_reference_availabel" value="no" /> - <param name="input_sample_file" ftype="bam" value="tumor.bam" /> - <param name="normal" ftype="bam" value="normal.bam" /> - <param name="targets" ftype="bed" value="capture.bed" /> - <param name="scatter" value="1"/> - <param name="diagram" value="1"/> + <section name="output_section"> + <param name="scatter" value="1"/> + <param name="diagram" value="1"/> + </section> <output name="out_sample_bintest" file="tumor.bintest.cns" /> <output name="out_sample_antitargetcoverage"> <assert_contents><has_text text="chromosome"/></assert_contents> @@ -233,11 +241,15 @@ </output> </test> <test expect_num_outputs="10"> - <param name="CNV_reference_availabel" value="yes" /> - <param name="input_sample_file" ftype="bam" value="tumor.bam" /> - <param name="reference" ftype="tabular" value="reference.cnn" /> - <param name="scatter" value="1"/> - <param name="diagram" value="1"/> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="yes" /> + <param name="input_sample_file" ftype="bam" value="tumor.bam" /> + <param name="reference" ftype="tabular" value="reference.cnn" /> + </conditional> + <section name="output_section"> + <param name="scatter" value="1"/> + <param name="diagram" value="1"/> + </section> <output name="out_sample_bintest" file="tumor.bintest.cns" /> <output name="out_sample_antitargetcoverage"> <assert_contents><has_text text="chromosome"/></assert_contents> |
| b |
| diff -r ec07e22c41f8 -r 97d2b6742760 macros.xml --- a/macros.xml Mon Apr 22 17:44:06 2024 +0000 +++ b/macros.xml Fri Dec 13 23:59:44 2024 +0000 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@TOOL_VERSION@">0.9.11</token> <xml name="requirements"> <requirements> |