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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit c508c3af0f4121dcc38e0be63db00a604e997b8a |
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modified:
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.hardclipped.bam |
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added:
test-data/eboVir3.clipped.strand_gt30.counts.tsv |
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| diff -r 4967154b9859 -r f597cb9b33bf macros.xml --- a/macros.xml Sun Sep 08 03:25:18 2024 +0000 +++ b/macros.xml Thu Jun 19 12:58:20 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 4967154b9859 -r f597cb9b33bf samtools_ampliconclip.xml --- a/samtools_ampliconclip.xml Sun Sep 08 03:25:18 2024 +0000 +++ b/samtools_ampliconclip.xml Thu Jun 19 12:58:20 2025 +0000 |
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| @@ -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> |
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| diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.bam |
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| Binary file test-data/eboVir3.clipped.bam has changed |
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| diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand.bam |
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| Binary file test-data/eboVir3.clipped.strand.bam has changed |
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| diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand_gt30.bam |
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| Binary file test-data/eboVir3.clipped.strand_gt30.bam has changed |
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| diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand_gt30.counts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eboVir3.clipped.strand_gt30.counts.tsv Thu Jun 19 12:58:20 2025 +0000 |
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| @@ -0,0 +1,4 @@ +#CHR LEFT RIGHT NAME SCORE STRAND NUM_CLIPPED +eboVir3 500 1500 1 0 - 113 +eboVir3 1500 2000 2 0 + 42 +eboVir3 1500 3000 3 0 - 141 |
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| diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.hardclipped.bam |
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| Binary file test-data/eboVir3.hardclipped.bam has changed |