|
49
|
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
|
|
52
|
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
|
|
49
|
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>
|
|
52
|
31 <data name="outfile" format="txt"/>
|
|
|
32 <data name="histogram_outfile" format="png">
|
|
|
33 <filter>histogram is True</filter>
|
|
49
|
34 </data>
|
|
|
35 </outputs>
|
|
52
|
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>
|
|
49
|
44 <help>
|
|
52
|
45 <![CDATA[
|
|
49
|
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@
|
|
52
|
53 ]]>
|
|
49
|
54 </help>
|
|
|
55 <expand macro="citations" />
|
|
|
56 </tool>
|
