Mercurial > repos > iuc > bedtools
diff intersectBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
---|---|
date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
children | 64e2edfe7a2c |
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--- a/intersectBed.xml Wed Jan 12 19:22:14 2022 +0000 +++ b/intersectBed.xml Fri Apr 01 19:02:51 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>find overlapping intervals in various ways</description> <macros> <import>macros.xml</import> @@ -51,6 +51,7 @@ $header $modes @SORTED@ +@GENOME_FILE@ $bed $count > '${output}' @@ -117,6 +118,7 @@ label="When using BAM input, write output as BED instead of BAM." /> <!-- -sorted -g --> <expand macro="sorted" /> + <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/> <expand macro="print_header" /> </inputs> <outputs> @@ -151,7 +153,7 @@ <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> </conditional> <param name="overlap_mode" value="-wa,-wb" /> - <param name="sorted" value="-sorted" /> + <param name="sorted" value="true" /> <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" /> </test> <test> @@ -163,7 +165,7 @@ <param name="names" value="yes" /> </conditional> <param name="overlap_mode" value="-wa,-wb" /> - <param name="sorted" value="-sorted" /> + <param name="sorted" value="true" /> <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" /> </test> <test> @@ -173,7 +175,7 @@ <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> </conditional> <param name="invert" value="-v" /> - <param name="sorted" value="-sorted" /> + <param name="sorted" value="true" /> <output name="output" file="intersect-multiple-invert.bed" ftype="bed" /> </test> <test> @@ -187,7 +189,7 @@ <param name="fraction_select" value="specify"/> <param name="overlap" value="1.0" /> </conditional> - <param name="sorted" value="-sorted" /> + <param name="sorted" value="true" /> <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" /> </test> <test>