Mercurial > repos > mvdbeek > size_distribution

comparison alignment_size_distribution.xml @ 1:3ed18dcb6f82 draft

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planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit a0c9f33672103cf29ad015477ebb898007ba9ae8
author mvdbeek
date Mon, 20 Aug 2018 13:00:14 -0400
parents ac5584567084
children c8c7b6113241
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0:ac5584567084 1:3ed18dcb6f82
3 <requirement type="package" version="6.7">click</requirement> 3 <requirement type="package" version="6.7">click</requirement>
4 <requirement type="package" version="0.23">pandas</requirement> 4 <requirement type="package" version="0.23">pandas</requirement>
5 <requirement type="package" version="0.15">pysam</requirement> 5 <requirement type="package" version="0.15">pysam</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution' 8 python '$__tool_directory__/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution'
9 ]]></command> 9 ]]></command>
10 <inputs> 10 <inputs>
11 <param name="alignment_file" type="data" format="bam,unsorted.bam"/> 11 <param name="alignment_file" type="data" format="bam,unsorted.bam"/>
12 <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/> 12 <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/>
13 <param argument="--maximum_size" type="integer" value="18" min="1" label="Maximum read length to consider"/> 13 <param argument="--maximum_size" type="integer" value="18" min="1" label="Maximum read length to consider"/>