Mercurial > repos > iuc > cnvkit_reference
changeset 4:b45fa373a972 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
| author | iuc |
|---|---|
| date | Fri, 13 Dec 2024 23:57:41 +0000 |
| parents | c6102e8e3deb |
| children | ee80db1d39c0 |
| files | macros.xml reference.xml |
| diffstat | 2 files changed, 64 insertions(+), 34 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Mon Apr 22 17:43:24 2024 +0000 +++ b/macros.xml Fri Dec 13 23:57:41 2024 +0000 @@ -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>
--- a/reference.xml Mon Apr 22 17:43:24 2024 +0000 +++ b/reference.xml Fri Dec 13 23:57:41 2024 +0000 @@ -98,60 +98,90 @@ </outputs> <tests> <test expect_num_outputs="1"> - <conditional name="reference_source"> - <param name="ref_selector" value="history"/> - <param name="fasta" ftype="fasta" value="genome.fasta" /> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="yes" /> + <section name="advanced_settings"> + <conditional name="reference_source"> + <param name="ref_selector" value="history"/> + <param name="fasta" ftype="fasta" value="genome.fasta" /> + </conditional> + </section> + <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> + <section name="disable_some_of_the_bias_corrections"> + <param name="no_gc" value="1" /> + </section> </conditional> - <param name="CNV_reference_availabel" value="yes" /> - <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> - <param name="no_gc" value="1" /> <output name="out_referene_tas" file="ref-tas.cnn" /> </test> <test expect_num_outputs="1"> - <conditional name="reference_source"> - <param name="ref_selector" value="cached"/> - <param name="fasta" value="test_buildid"/> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="yes" /> + <section name="advanced_settings"> + <conditional name="reference_source"> + <param name="ref_selector" value="cached"/> + <param name="fasta" value="test_buildid"/> + </conditional> + </section> + <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> + <section name="disable_some_of_the_bias_corrections"> + <param name="no_gc" value="1" /> + </section> </conditional> - <param name="CNV_reference_availabel" value="yes" /> - <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> - <param name="no_gc" value="1" /> <output name="out_referene_tas" file="ref-tas.cnn" /> </test> <test expect_num_outputs="1"> - <conditional name="reference_source"> - <param name="ref_selector" value="cached"/> - <param name="fasta" value="test_buildid"/> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="yes" /> + <section name="advanced_settings"> + <conditional name="reference_source"> + <param name="ref_selector" value="cached"/> + <param name="fasta" value="test_buildid"/> + </conditional> + </section> + <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" /> + <section name="disable_some_of_the_bias_corrections"> + <param name="no_gc" value="1" /> + </section> </conditional> - <param name="CNV_reference_availabel" value="yes" /> - <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" /> - <param name="no_gc" value="1" /> <output name="out_referene_tas"> <assert_contents><has_text text="chromosome"/></assert_contents> </output> </test> <test expect_num_outputs="1"> - <conditional name="reference_source"> - <param name="ref_selector" value="cached"/> - <param name="fasta" value="test_buildid"/> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="no" /> + <section name="advanced_settings"> + <conditional name="reference_source"> + <param name="ref_selector" value="cached"/> + <param name="fasta" value="test_buildid"/> + </conditional> + </section> + <param name="targets" ftype="bed" value="capture.target.bed" /> + <section name="disable_some_of_the_bias_corrections"> + <param name="no_gc" value="1" /> + </section> </conditional> - <param name="CNV_reference_availabel" value="no" /> - <param name="targets" ftype="bed" value="capture.target.bed" /> - <param name="no_gc" value="1" /> <output name="out_referene_tas"> <assert_contents><has_text text="chromosome"/></assert_contents> </output> </test> <test expect_num_outputs="1"> - <conditional name="reference_source"> - <param name="ref_selector" value="cached"/> - <param name="fasta" value="test_buildid"/> + <conditional name="CNV_reference"> + <param name="CNV_reference_availabel" value="no" /> + <section name="advanced_settings"> + <conditional name="reference_source"> + <param name="ref_selector" value="cached"/> + <param name="fasta" value="test_buildid"/> + </conditional> + <conditional name="Sample_sex"> + <param name="sex" value="no" /> + </conditional> + </section> + <param name="targets" ftype="bed" value="capture.target.bed" /> + <section name="disable_some_of_the_bias_corrections"> + <param name="no_gc" value="1" /> + </section> </conditional> - <conditional name="Sample_sex"> - <param name="sex" value="no" /> - </conditional> - <param name="CNV_reference_availabel" value="no" /> - <param name="targets" ftype="bed" value="capture.target.bed" /> - <param name="no_gc" value="1" /> <output name="out_referene_tas"> <assert_contents><has_text text="chromosome"/></assert_contents> </output>