Mercurial > repos > iuc > bedtools

comparison bedpeToBam.xml @ 64:f6c88d2e9ae5 draft default tip

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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 9f6bd4c9479f
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>converter</description> 2 <description>converter</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools" />
7 <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> --> 7 <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
8 <requirements> 8 <requirements>
9 <requirement type="package" version="2.27.1">bedtools</requirement> 9 <requirement type="package" version="2.31.1">bedtools</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 bedtools bedpetobam 13 bedtools bedpetobam
14 -mapq $mapq 14 -mapq $mapq
26 <data name="output" format="unsorted.bam" metadata_source="input"/> 26 <data name="output" format="unsorted.bam" metadata_source="input"/>
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test> 29 <test>
30 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> 30 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
31 <param name="genome_file_opts_selector" value="hist" /> 31 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
32 <param name="genome" value="mm9.len"/> 32 <param name="genome_file_opts|genome" value="mm9.len"/>
33 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" /> 33 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
34 </test> 34 </test>
35 </tests> 35 </tests>
36 <help><![CDATA[ 36 <help><![CDATA[
37 **What it does** 37 **What it does**