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comparison readmap.xml @ 10:be6fb196f074 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 8da4eb1a48d56a8186ba3ca33d3de73aff8da323
author drosofff
date Tue, 19 Dec 2017 11:52:57 -0500
parents 92898cc3ea19
children 791edb7b7ea1
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9:92898cc3ea19 10:be6fb196f074
1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.0"> 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.1">
2 <description>from sRbowtie aligment</description> 2 <description>from sRbowtie aligment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 <requirement type="package" version="0.9.0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.9.3">numpy</requirement> 6 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
7 <requirement type="package" version="1.3.0=r3.2.2_1">r-optparse</requirement> 7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
8 <requirement type="package" version="0.6_26=r3.2.2_2a">r-latticeextra</requirement> 8 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
9 <requirement type="package" version="2.0.0=r3.2.2_0a">r-gridextra</requirement> 9 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
10
10 </requirements> 11 </requirements>
11 <command><![CDATA[ 12 <command><![CDATA[
12 python2 $__tool_directory__/readmap.py 13 python2 $__tool_directory__/readmap.py
13 #if $refGenomeSource.genomeSource == "history": 14 #if $refGenomeSource.genomeSource == "history":
14 --reference_fasta 15 --reference_fasta
129 ---- 130 ----
130 131
131 .. image:: static/images/readmap.png 132 .. image:: static/images/readmap.png
132 :height: 800 133 :height: 800
133 :width: 500 134 :width: 500
134
135 </help> 135 </help>
136 <tests> 136 <tests>
137 <test> 137 <test>
138 <param name="genomeSource" value="history" /> 138 <param name="genomeSource" value="history" />
139 <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> 139 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />