Mercurial > repos > kyost > atac_primer_tool
comparison filter_bam.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="filter_bam" name="Filter bam files" version="0.1.0"> | |
2 <description> Filters bam files for reads in regions 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_name = str( $input1.name ) | |
12 $__tool_directory__/./filter_bam.bash "$input1" "$input2" "$input3" "$output1" "$output2" "$output3" "$input_name" | |
13 ]]></command> | |
14 <inputs> | |
15 <param type="data" name="input1" format="bam" label="Bam File"/> | |
16 <param type="data" name="input2" format="bed" label="Peak Bed File"/> | |
17 <param type="data" name="input3" format="tabular" label="chrom.sizes"/> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="output1" format="bed" label="Extended Peak File"/> | |
21 <data name="output2" format="bam" label="Filtered Bam File"/> | |
22 <data name="output3" format="tabular" label="Read Counts" /> | |
23 </outputs> | |
24 <tests> | |
25 <test> | |
26 <param name="input1" value="test.bam"/> | |
27 <param name="input2" value="test.bed"/> | |
28 <param name="input3" value="mm9.chrom.sizes.txt"/> | |
29 <output name="output1" file="ext_peak"/> | |
30 <output name="output2" file="test.filter.bam"/> | |
31 <output name="output3" file="test.readcounts.txt"/> | |
32 </test> | |
33 </tests> | |
34 <help><![CDATA[ | |
35 This tools takes a bam file and filters to reads mapping to regions specified by input bed file. Outputs include filtered bam file and count of total numbers of reads in original bam file. | |
36 ]]></help> | |
37 <citations> | |
38 <citation type="doi">doi:10.1038/nmeth.4663</citation> | |
39 </citations> | |
40 </tool> |