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comparison bamPEFragmentSize.xml @ 0:b2886915ce68 draft default tip

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author bgruening
date Tue, 10 Feb 2015 03:21:34 -0500
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-1:000000000000 0:b2886915ce68
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 @THREADS@
13 -bai ${bamInput.metadata.bam_index}
14 #if $histogram:
15 --histogram ./hist.png
16 #end if
17 '$bamInput'
18 > $outfile
19 &&
20 mv ./hist.png $histogram_outfile
21 ]]>
22 </command>
23 <inputs>
24 <param name="bamInput" format="bam" type="data" label="BAM file"
25 help="The BAM file must be sorted."/>
26 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
27 label="Get the distribion of fragment length as histogram"
28 help="(--histogram)"/>
29 </inputs>
30 <outputs>
31 <data name="outfile" format="txt"/>
32 <data name="histogram_outfile" format="png">
33 <filter>histogram is True</filter>
34 </data>
35 </outputs>
36 <tests>
37 <test>
38 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
39 <param name="histogram" value="True" />
40 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
41 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" />
42 </test>
43 </tests>
44 <help>
45 <![CDATA[
46 **What it does**
47
48 Given a BAM file it samples several regions to estimate the paird-end fragment length.
49
50 -----
51
52 @REFERENCES@
53 ]]>
54 </help>
55 <expand macro="citations" />
56 </tool>