Mercurial > repos > iuc > samtools_coverage
changeset 5:ddbd49b892e5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a
| author | iuc |
|---|---|
| date | Thu, 19 Jun 2025 12:58:44 +0000 |
| parents | f4f7f632815d |
| children | |
| files | macros.xml samtools_coverage.xml |
| diffstat | 2 files changed, 34 insertions(+), 15 deletions(-) [+] |
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--- a/macros.xml Fri May 16 12:57:31 2025 +0000 +++ b/macros.xml Thu Jun 19 12:58:44 2025 +0000 @@ -11,8 +11,8 @@ please only bump the minor version in order to let the requirement version catch up eventually). To find the tools check: `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> - <token name="@TOOL_VERSION@">1.20</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">1.21</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 @@ -220,6 +220,7 @@ <xml name="citations"> <citations> <citation type="doi">10.1093/gigascience/giab008</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> </citations> </xml> <xml name="version_command">
--- a/samtools_coverage.xml Fri May 16 12:57:31 2025 +0000 +++ b/samtools_coverage.xml Thu Jun 19 12:58:44 2025 +0000 @@ -100,31 +100,49 @@ <tests> <test> - <param name="input" value="test_1.bam" ftype="bam" /> + <conditional name="condition_input"> + <param name="input" value="test_1.bam" ftype="bam" /> + </conditional> <output name="output" file="results_1.tabular" ftype="tabular" /> </test> <test> - <param name="input" value="test_1.bam" ftype="bam" /> - <param name="histogram_select" value="yes" /> - <param name="n_bins" value="50" /> + <conditional name="condition_input"> + <param name="input" value="test_1.bam" ftype="bam" /> + </conditional> + <conditional name="condition_histogram"> + <param name="histogram_select" value="yes" /> + <param name="n_bins" value="50" /> + </conditional> <output name="output" file="results_2.txt" ftype="tabular" /> </test> <test> - <param name="input_pooling" value="Yes" /> - <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> - <param name="histogram_select" value="yes" /> - <param name="n_bins" value="100" /> + <conditional name="condition_input"> + <param name="input_pooling" value="Yes" /> + <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> + </conditional> + <conditional name="condition_histogram"> + <param name="histogram_select" value="yes" /> + <param name="n_bins" value="100" /> + </conditional> <output name="output" file="results_3.txt" ftype="tabular" /> </test> <test><!-- test with a region (requires index) --> - <param name="input" value="test_1.bam" ftype="bam" /> - <param name="region" value="ref1" /> + <conditional name="condition_input"> + <param name="input" value="test_1.bam" ftype="bam" /> + </conditional> + <section name="additional_options"> + <param name="region" value="ref1" /> + </section> <output name="output" file="results_4.tabular" ftype="tabular" /> </test> <test><!-- test with pooled BAMs and a region --> - <param name="input_pooling" value="Yes" /> - <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> - <param name="region" value="ref2" /> + <conditional name="condition_input"> + <param name="input_pooling" value="Yes" /> + <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> + </conditional> + <section name="additional_options"> + <param name="region" value="ref2" /> + </section> <output name="output" file="results_5.tabular" ftype="tabular" /> </test> </tests>