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comparison bamToBed.xml @ 55:678ea22d643d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
author iuc
date Thu, 06 May 2021 14:14:33 +0000
parents b4cf5fca8773
children 7a06bb42dbb1
comparison
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54:b06c53665eb6 55:678ea22d643d
1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@"> 1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1">
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="requirements"> 6 <expand macro="requirements">
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 in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
12 samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input && 12 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
13 #else 13 #else
14 ln -s '${input}' ./input.bam && 14 ln -s '${input}' ./input.bam &&
15 #end if 15 #end if
16 16
17 bedtools bamtobed 17 bedtools bamtobed
23 #end if 23 #end if
24 -i ./input.bam 24 -i ./input.bam
25 > '${output}' 25 > '${output}'
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/> 28 <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
29 <param name="option" type="select" label="What type of BED output would you like"> 29 <param name="option" type="select" label="What type of BED output would you like">
30 <option value="">Create a 6-column BED file</option> 30 <option value="">Create a 6-column BED file</option>
31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option> 31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
32 <option value="-bedpe">Create a paired-end, BEDPE format</option> 32 <option value="-bedpe">Create a paired-end, BEDPE format</option>
33 </param> 33 </param>