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comparison bamToBed.xml @ 41:7ab85ac5f64b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:36:55 +0000
parents 3e38c9b3214f
children 64e2edfe7a2c
comparison
equal deleted inserted replaced
40:a68aa6c1204a 41:7ab85ac5f64b
1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>converter</description> 2 <description>converter</description>
3 <expand macro="bio_tools" />
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools" />
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> 8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
9 </expand> 9 </expand>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": 12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input && 13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam &&
14 #else 14 #else
15 ln -s '${input}' ./input.bam && 15 ln -s '${input}' ./input.bam &&
16 #end if 16 #end if
17 17
18 bedtools bamtobed 18 bedtools bamtobed
52 <param name="input" value="srma_in3.bam" ftype="bam" /> 52 <param name="input" value="srma_in3.bam" ftype="bam" />
53 <param name="option" value="" /> 53 <param name="option" value="" />
54 <param name="tag" value="NM" /> 54 <param name="tag" value="NM" />
55 <output name="output" file="bamToBed_result2.bed" ftype="bed" /> 55 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
56 </test> 56 </test>
57 <test>
58 <param name="input" value="bedpeToBam_result1.bam" ftype="bam" />
59 <param name="option" value="-bedpe" />
60 <param name="tag" value="" />
61 <output name="output" file="bamToBed_result3.bed" ftype="bed" />
62 </test>
57 </tests> 63 </tests>
58 <help><![CDATA[ 64 <help><![CDATA[
59 **What it does** 65 **What it does**
60 66
61 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. 67 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.