Mercurial > repos > iuc > samtools_ampliconclip
changeset 4:f597cb9b33bf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author | iuc |
---|---|
date | Thu, 19 Jun 2025 12:58:20 +0000 |
parents | 4967154b9859 |
children | |
files | macros.xml samtools_ampliconclip.xml test-data/eboVir3.clipped.bam test-data/eboVir3.clipped.strand.bam test-data/eboVir3.clipped.strand_gt30.bam test-data/eboVir3.clipped.strand_gt30.counts.tsv test-data/eboVir3.hardclipped.bam |
diffstat | 7 files changed, 12 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Sun Sep 08 03:25:18 2024 +0000 +++ b/macros.xml Thu Jun 19 12:58:20 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_ampliconclip.xml Sun Sep 08 03:25:18 2024 +0000 +++ b/samtools_ampliconclip.xml Thu Jun 19 12:58:20 2025 +0000 @@ -50,14 +50,14 @@ <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bam" value="eboVir3.bam" ftype="bam" /> - <param name="strand" value="--strand" /> + <param name="strand" value="true" /> <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" /> </test> <!-- 3) testing hard clip--> <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bam" value="eboVir3.bam" ftype="bam" /> - <param name="hard_clip_mode" value="--hard-clip" /> + <param name="hard_clip_mode" value="true" /> <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" /> </test> <!-- 4) testing strand and min length--> @@ -65,10 +65,10 @@ <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bam" value="eboVir3.bam" ftype="bam" /> <param name="min_length" value="30" /> - <param name="strand" value="--strand" /> + <param name="strand" value="true" /> <param name="tolerance" value="6" /> - <param name="both_ends" value="--both-ends" /> - <param name="no_excluded" value="--no-excluded" /> + <param name="both_ends" value="true" /> + <param name="no_excluded" value="true" /> <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" /> </test>