Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison bamPEFragmentSize.xml @ 1:011ea45dda07 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:25:00 -0500
parents bb2b0ad44c0e
children 6da6f2908463
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0:bb2b0ad44c0e 1:011ea45dda07
1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
2 <description>Estimate the paired-end fragment length in a BAM file</description> 2 <description>Estimate the predominant cDNA fragment length from a paired-end sequenced BAM file</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">bamPEFragmentSize</token> 4 <token name="@BINARY@">bamPEFragmentSize</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
14 @THREADS@ 14 @THREADS@
15 #if $histogram: 15 #if $histogram:
16 --histogram ./hist.png 16 --histogram ./hist.png
17 #end if 17 #end if
18 --plotTitle "$plotTitle" 18 --plotTitle "$plotTitle"
19 #if $advancedOpt.showAdvancedOpt == 'yes'
20 --binSize '$advancedOpt.binSize'
21 --distanceBetweenBins '$advancedOpt.distanceBetweenBins'
22 #end if
19 one.bam 23 one.bam
20 > $outfile 24 > $outfile
21 ]]> 25 ]]>
22 </command> 26 </command>
23 <inputs> 27 <inputs>
25 help="The BAM file must be sorted."/> 29 help="The BAM file must be sorted."/>
26 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" 30 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
27 label="Get the distribution of fragment lengths as a histogram" 31 label="Get the distribution of fragment lengths as a histogram"
28 help=""/> 32 help=""/>
29 <expand macro="plotTitle" /> 33 <expand macro="plotTitle" />
34 <conditional name="advancedOpt">
35 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
36 <option value="no" selected="true">no</option>
37 <option value="yes">yes</option>
38 </param>
39 <when value="no" />
40 <when value="yes">
41 <param argument="--binSize" type="integer" value="1000" min="1" optional="true"
42 label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
43 <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true"
44 label="bin spacing, in bases"
45 help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/>
46 </when>
47 </conditional>
48
30 </inputs> 49 </inputs>
31 <outputs> 50 <outputs>
32 <data name="outfile" format="txt"/> 51 <data name="outfile" format="txt"/>
33 <data name="histogram_outfile" from_work_dir="hist.png" format="png"> 52 <data name="histogram_outfile" from_work_dir="hist.png" format="png">
34 <filter>histogram is True</filter> 53 <filter>histogram is True</filter>
43 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" /> 62 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
44 </test> 63 </test>
45 </tests> 64 </tests>
46 <help> 65 <help>
47 <![CDATA[ 66 <![CDATA[
48 **What it does**
49 67
50 This tool samples a BAM file containing paired-end data to estimate the fragment length distribution. 68 What it does
51 Properly paired reads are preferred for computation. The output can be obtained as a histogram. 69 ---------------
70
71 This tool samples a BAM file with paired-end data to estimate the fragment length distribution.
72 Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored.
73
74 Output
75 ----------
76
77 The **default** output is a simple summary statistic for the observed fragment lengths.
78
79 Optionally, you can obtain a histogram of fragment sizes, which will give you a better idea of the distribution of fragment lengths.
80
81 .. image:: $PATH_TO_IMAGES/bamPEFragmentSize_output.png
82 :width: 600
83 :height: 520
84
52 85
53 ----- 86 -----
54 87
55 @REFERENCES@ 88 @REFERENCES@
56 ]]> 89 ]]>