Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison bamPEFragmentSize.xml @ 8:dc8d6e07d829 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Mon, 19 Sep 2016 17:25:47 -0400
parents a14f74993305
children 0ed472892e76
comparison
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7:b4886e1369c4 8:dc8d6e07d829
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 predominant cDNA fragment length from a paired-end sequenced BAM file</description> 2 <description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM files</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" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ln -s $bamInput one.bam && 10 @multiple_input_bams@
11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
12
13 @BINARY@ 11 @BINARY@
14 @THREADS@ 12 @THREADS@
13 --bamfiles #echo " ".join($files)
14 #if $samplesLabel:
15 --samplesLabel #echo " ".join($samplesLabel)
16 #end if
15 #if $histogram: 17 #if $histogram:
16 --histogram ./hist.png 18 --histogram ./hist.png
17 #end if 19 #end if
18 --plotTitle "$plotTitle" 20 --plotTitle "$plotTitle"
19 #if $advancedOpt.showAdvancedOpt == 'yes' 21 #if $advancedOpt.showAdvancedOpt == 'yes'
20 --binSize '$advancedOpt.binSize' 22 --binSize '$advancedOpt.binSize'
21 --distanceBetweenBins '$advancedOpt.distanceBetweenBins' 23 --distanceBetweenBins '$advancedOpt.distanceBetweenBins'
24 $advancedOpt.logScale
25 --maxFragmentLength '$advancedOpt.maxFragmentLength'
26 @blacklist@
22 #end if 27 #end if
23 one.bam
24 > $outfile 28 > $outfile
25 ]]> 29 ]]>
26 </command> 30 </command>
27 <inputs> 31 <inputs>
28 <param name="bamInput" format="bam" type="data" label="BAM file" 32 <expand macro="multiple_input_bams" />
29 help=""/>
30 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" 33 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
31 label="Get the distribution of fragment lengths as a histogram" 34 label="Get the distribution of fragment lengths as a histogram"
32 help=""/> 35 help=""/>
36 <param argument="--samplesLabel" type="text" size="30"
37 label="Labels for the samples (each BAM file) plotted"
38 help="The default is to use the file name of the sample. The sample labels should be separated by
39 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
40 <sanitizer>
41 <valid initial="string.printable">
42 </valid>
43 </sanitizer>
44 </param>
33 <expand macro="plotTitle" /> 45 <expand macro="plotTitle" />
34 <conditional name="advancedOpt"> 46 <conditional name="advancedOpt">
35 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 47 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
36 <option value="no" selected="true">no</option> 48 <option value="no" selected="true">no</option>
37 <option value="yes">yes</option> 49 <option value="yes">yes</option>
41 <param argument="--binSize" type="integer" value="1000" min="1" optional="true" 53 <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)"/> 54 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" 55 <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true"
44 label="bin spacing, in bases" 56 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)"/> 57 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)"/>
58 <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
59 label="Plot log frequencies"
60 help="Plot the frequencies on the log10 scale" />
61
62 <param argument="--maxFragmentLength" type="integer" min="0" value="0"
63 label="Maximum fragment length"
64 help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length" />
65 <expand macro="blacklist" />
46 </when> 66 </when>
47 </conditional> 67 </conditional>
48 68
49 </inputs> 69 </inputs>
50 <outputs> 70 <outputs>
53 <filter>histogram is True</filter> 73 <filter>histogram is True</filter>
54 </data> 74 </data>
55 </outputs> 75 </outputs>
56 <tests> 76 <tests>
57 <test> 77 <test>
58 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" /> 78 <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam" />
59 <param name="histogram" value="True" /> 79 <param name="histogram" value="True" />
60 <param name="plotTitle" value="Test Plot" /> 80 <param name="plotTitle" value="Test Plot" />
61 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> 81 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
62 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" /> 82 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
63 </test> 83 </test>
66 <![CDATA[ 86 <![CDATA[
67 87
68 What it does 88 What it does
69 ------------ 89 ------------
70 90
71 This tool samples a BAM file with paired-end data to estimate the fragment length distribution. 91 This tool samples the given BAM files 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. 92 Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored.
73 93
74 Output 94 Output
75 ------ 95 ------
76 96