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comparison window_coverage.xml @ 0:fd3ea97a96bc draft

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Sat, 28 Apr 2018 15:07:26 -0400
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1 <tool id="window_coverage" name="Calculate window coverage" version="0.1.0">
2 <description> Determines spanning and total read coverage for overlapping windows spanning peaks of interest. </description>
3 <requirements>
4 <requirement type="package" version="1.3">samtools</requirement>
5 <requirement type="package" version="2.27.0.0">bedtools</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command><![CDATA[
11 #set input_list = '","'.join( [str( $input.name ) for $input in $input1 ] )
12 $__tool_directory__/./window_coverage.bash "$input1" "$input_list" "$input2" "$input3" "$output1" "$output2"
13 ]]></command>
14 <inputs>
15 <param type="data" name="input1" format="bam" multiple="true" label="Filtered Bam Files"/>
16 <param type="data" name="input2" format="bed" label="qPCR Window Bed File"/>
17 <param type="float" name="input3" value="0.9" label="Coverage Cutoff"/>
18 </inputs>
19 <outputs>
20 <data name="output1" format="bed" label="Coverage Bed File"/>
21 <data name="output2" format="bed" label="Spanning Fragment Coverage Bed File" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input1" value="Ch1-1.pe.q10.sort.bam.rmdup.filter.bam,Ch13-1.pe.q10.sort.rmdup.filter.bam"/>
26 <param name="input2" value="qPCR_windows.bed" />
27 <param name="input3" value="0.9" />
28 <output name="output1" file="combined.o.coverage"/>
29 <output name="output2" file="combined.f9.coverage"/>
30 </test>
31 </tests>
32 <help><![CDATA[
33 This tools takes a series of bam files and a bed file of overlapping windows spanning peaks of interest and determines the read coverage and spanning fragment coverage for each window.
34 ]]></help>
35 <citations>
36 <citation type="doi">doi:10.1038/nmeth.4663</citation>
37 </citations>
38 </tool>