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comparison pe_histogram.xml @ 4:784273cfcebc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
author iuc
date Wed, 04 Dec 2019 13:17:44 +0000
parents 99c86046c72a
children 551f36b118b1
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3:99c86046c72a 4:784273cfcebc
1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> 1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1">
2 <description>of insert size frequency</description> 2 <description>of insert size frequency</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.0.112">openjdk</requirement> 4 <requirement type="package" version="11.0.1">openjdk</requirement>
5 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
7 ln -s '${input_bam}' localbam.bam && 8 ln -s '${input_bam}' localbam.bam &&
8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai && 9 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
9 java -jar '$__tool_directory__/PEHistogram.jar' 10 java -jar '$__tool_directory__/PEHistogram.jar'
19 -t '$output2' 20 -t '$output2'
20 1>/dev/null 21 1>/dev/null
21 ]]></command> 22 ]]></command>
22 <inputs> 23 <inputs>
23 <param name="input_bam" type="data" format="bam" label="BAM file" /> 24 <param name="input_bam" type="data" format="bam" label="BAM file" />
24 <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/> 25 <param name="lower_limit" type="integer" value="" optional="true" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
25 <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." /> 26 <param name="upper_limit" type="integer" value="" optional="true" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
26 </inputs> 27 </inputs>
27 <outputs> 28 <outputs>
28 <data name="output1" format="png" /> 29 <data name="output1" format="png" />
29 <data name="output2" format="tabular" /> 30 <data name="output2" format="tabular" />
30 </outputs> 31 </outputs>