Mercurial > repos > kyost > atac_primer_tool
comparison window_coverage.xml @ 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author | kyost |
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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> |