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comparison bamPEFragmentSize.xml @ 29:3a2aab18a217 draft

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author bgruening
date Tue, 16 Sep 2014 13:46:05 -0400
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children 5231f398d784
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28:f7712a057440 29:3a2aab18a217
1 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
2 <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">bamPEFragmentSize</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 <![CDATA[
11 bamPEFragmentSize
12
13 @THREADS@
14
15 --bam '$bamInput'
16 --bamIndex ${bamInput.metadata.bam_index}
17 #if $histogram:
18 --histogram $histogram_outfile
19 #end if
20 > $outfile
21
22 ]]>
23 </command>
24
25 <inputs>
26 <param name="bamInput" format="bam" type="data" label="BAM file"
27 help="The BAM file must be sorted."/>
28 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
29 label="Get the distribion of fragment length as histogram"
30 help="(--histogram)"/>
31 </inputs>
32 <outputs>
33 <data format="txt" name="outfile" label="${tool.name} on ${on_string}" />
34 <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
35 <filter>histogram == '--histogram'</filter>
36 </data>
37 </outputs>
38 <help>
39
40 **What it does**
41
42 Given a BAM file it samples several regions to estimate the paird-end fragment length.
43
44 -----
45
46 @REFERENCES@
47
48 </help>
49 <expand macro="citations" />
50 </tool>