Mercurial > repos > bgruening > deeptools

comparison correctGCBias.xml @ 1:21d563d5f2b2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 05 Aug 2013 10:09:51 -0400
parents 09b65c12a75a
children 1f312af2f8db
comparison
equal deleted inserted replaced
0:09b65c12a75a 1:21d563d5f2b2
1 <tool id="correctGCBias" name="correctGCBias" version="1.0"> 1 <tool id="correctGCBias" name="correctGCBias" version="1.0.1">
2 <description> 2 <description>
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement> 5 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
6 <requirement type="package" version="0.1">ucsc_tools</requirement> 6 <requirement type="package" version="0.1">ucsc_tools</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 #import tempfile
10 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
11
12 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
13 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
14 #silent $temp_bam_handle.close()
15 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
16 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
17
18
9 correctGCBias 19 correctGCBias
10 --bamfile '$bamInput' 20 --bamfile '$temp_bam_path'
11 --species '$species' 21 --species '$species'
12 --GCbiasFrequenciesFile $GCbiasFrequenciesFile 22 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
13 23
14 #if $source.ref_source=="history": 24 #if $source.ref_source=="history":
15 --genome $source.input1 25 --genome $source.input1
30 --correctedFile $newoutFileName; mv $newoutFileName $outFileName 40 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
31 41
32 </command> 42 </command>
33 43
34 <inputs> 44 <inputs>
35 45
36 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> 46 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
37 47
38 <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/> 48 <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
39 49
40 <param name="species" type="text" value="" label="Species name abbreviation" /> 50 <param name="species" type="select" label="Species name abbreviation">
41 51 <option value="hg19">hg19</option>
52 <option value="ce10">ce10</option>
53 <option value="dm3">dm3</option>
54 <option value="mm9">mm9</option>
55 </param>
56
42 <conditional name="source"> 57 <conditional name="source">
43 <param name="ref_source" type="select" label="Reference genome"> 58 <param name="ref_source" type="select" label="Reference genome">
44 <option value="cached">locally cached</option> 59 <option value="cached">locally cached</option>
45 <option value="history">in your history</option> 60 <option value="history">in your history</option>
46 </param> 61 </param>