Mercurial > repos > iuc > bedtools
diff jaccardBed.xml @ 64:f6c88d2e9ae5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
| author | iuc |
|---|---|
| date | Fri, 21 Feb 2025 21:38:34 +0000 |
| parents | 539958feb49c |
| children |
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--- a/jaccardBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/jaccardBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="bio_tools" /> - <expand macro="requirements" /> - <expand macro="stdio" /> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ bedtools jaccard $strand @@ -22,29 +22,33 @@ <inputs> <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> - <expand macro="overlap" /> + <expand macro="overlap"/> <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> - <expand macro="reciprocal" /> - <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" - label="Force strandedness" - help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." /> - <expand macro="strand2" /> - <expand macro="split" /> + <expand macro="reciprocal"/> + <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand."/> + <expand macro="split"/> </inputs> <outputs> - <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> + <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/> </outputs> <tests> <test> - <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> - <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> - <output name="output" file="jaccardBed_result1.bed" ftype="bed" /> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <output name="output" file="jaccardBed_result1.bed" ftype="bed"/> </test> <test> - <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> - <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> - <param name="overlap" value="0.1" /> - <output name="output" file="jaccardBed_result2.bed" ftype="bed" /> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <param name="overlap" value="0.1"/> + <output name="output" file="jaccardBed_result2.bed" ftype="bed"/> + </test> + <test> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <param name="overlap" value="0.1"/> + <param name="strand" value="true"/> + <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/> </test> </tests> <help><![CDATA[ @@ -61,5 +65,5 @@ @REFERENCES@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>