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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a |
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modified:
macros.xml sam_to_bam.xml |
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| diff -r 0e60e2dd20af -r 73913bb77da3 macros.xml --- a/macros.xml Sun Sep 08 03:25:11 2024 +0000 +++ b/macros.xml Thu Jun 19 12:58:11 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 0e60e2dd20af -r 73913bb77da3 sam_to_bam.xml --- a/sam_to_bam.xml Sun Sep 08 03:25:11 2024 +0000 +++ b/sam_to_bam.xml Thu Jun 19 12:58:11 2025 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.3" profile="@PROFILE@"> <description>convert SAM to BAM</description> <macros> @@ -50,34 +50,44 @@ </outputs> <tests> <test> - <param name="addref_select" value="history" /> - <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> + </conditional> <param name="input" ftype="sam" value="sam_to_bam_in1.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/> </test> <test> - <param name="addref_select" value="cached" /> - <param name="ref" value="equCab2chrM" /> + <conditional name="addref_cond"> + <param name="addref_select" value="cached" /> + <param name="ref" value="equCab2chrM" /> + </conditional> <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/> </test> <test> - <param name="addref_select" value="history" /> - <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> + </conditional> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> <test> <!-- Test direct use of bgzipped reference --> - <param name="addref_select" value="history" /> - <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> + </conditional> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> <test> <!-- Test with simple gzipped reference, which requires decompression --> - <param name="addref_select" value="history" /> - <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> + <conditional name="addref_cond"> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> + </conditional> <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> |