Mercurial > repos > iuc > bedtools

comparison bamToBed.xml @ 35:b28e0cfa7ba1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:29:59 -0400
parents dde39ba9c031
children fe5b4cb8356c
comparison
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34:dde39ba9c031 35:b28e0cfa7ba1
7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> 7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
8 </expand> 8 </expand>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <command><![CDATA[ 10 <command><![CDATA[
11 #if $input.extension == 'bam' and $option == "-bedpe": 11 #if $input.extension == 'bam' and $option == "-bedpe":
12 samtools sort -n '${input}' ./input && 12 samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
13 #else 13 #else
14 ln -s '${input}' ./input.bam && 14 ln -s '${input}' ./input.bam &&
15 #end if 15 #end if
16 16
17 bedtools bamtobed 17 bedtools bamtobed