| Previous changeset 8:18dbde5680c0 (2024-09-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit c508c3af0f4121dcc38e0be63db00a604e997b8a |
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modified:
macros.xml samtools_bam_to_cram.xml |
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| diff -r 18dbde5680c0 -r 85a38dffb93d macros.xml --- a/macros.xml Sun Sep 08 03:24:49 2024 +0000 +++ b/macros.xml Thu Jun 19 12:57:45 2025 +0000 |
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| @@ -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"> |
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| diff -r 18dbde5680c0 -r 85a38dffb93d samtools_bam_to_cram.xml --- a/samtools_bam_to_cram.xml Sun Sep 08 03:24:49 2024 +0000 +++ b/samtools_bam_to_cram.xml Thu Jun 19 12:57:45 2025 +0000 |
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| @@ -59,39 +59,59 @@ <tests> <test> <param name="input" value="test.bam" ftype="bam" /> - <param name="addref_select" value="history" /> - <param name="ref" value="test.fa" /> - <param name="target_region" value="entire_input_file" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" value="entire_input_file" /> + </conditional> <output name="output_alignment" file="test_bam.cram" ftype="cram" compare="sim_size" delta="250" /> </test> <test> <param name="input" value="test.sam" ftype="sam" /> - <param name="addref_select" value="history" /> - <param name="ref" value="test.fa" /> - <param name="target_region" value="entire_input_file" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" value="entire_input_file" /> + </conditional> <output name="output_alignment" file="test_sam.cram" ftype="cram" compare="sim_size" delta="250" /> </test> <test> <param name="input" value="test.bam" ftype="bam" /> - <param name="addref_select" value="history" /> - <param name="ref" value="test.fa" /> - <param name="target_region" value="region" /> - <param name="region_string" value="CHROMOSOME_I" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" value="region" /> + <param name="region_string" value="CHROMOSOME_I" /> + </conditional> <output name="output_alignment" file="test_chr1.cram" ftype="cram" compare="sim_size" delta="250" /> </test> <test> <param name="input" value="test.bam" ftype="bam" /> - <param name="addref_select" value="history" /> - <param name="ref" value="test.fa" /> - <param name="target_region" value="regions_bed_file" /> - <param name="regions_bed_file" value="test.bed" ftype="bed" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" value="regions_bed_file" /> + <param name="regions_bed_file" value="test.bed" ftype="bed" /> + </conditional> <output name="output_alignment" file="test_regions.cram" ftype="cram" compare="sim_size" delta="250" /> </test> <test> <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> - <param name="addref_select" value="cached" /> - <param name="ref" value="equCab2chrM" /> - <param name="target_region" value="entire_input_file" /> + <conditional name="addref_cond"> + <param name="addref_select" value="cached" /> + <param name="ref" value="equCab2chrM" /> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" value="entire_input_file" /> + </conditional> <output name="output_alignment" file="test2.cram" ftype="cram" compare="sim_size" delta="250" /> </test> </tests> |