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comparison correctGCBias.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
2 <description>uses the output from computeGCBias to generate corrected BAM files</description> 2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">correctGCBias</token> 4 <token name="@BINARY@">correctGCBias</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
9 <command> 8 <command>
10 #import tempfile 9 <![CDATA[
11 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) 10 ln -s $bamInput local_bamInput.bam;
12 11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
13 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
14 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
15 #silent $temp_bam_handle.close()
16 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
17 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
18
19 12
20 correctGCBias 13 correctGCBias
14 @THREADS@
15 --bamfile local_bamInput.bam
16 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
21 17
22 @THREADS@ 18 @reference_genome_source@
23 19
24 --bamfile '$temp_bam_path' 20 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
25 --GCbiasFrequenciesFile $GCbiasFrequenciesFile 21 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
22 #else:
23 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
24 #end if
26 25
27 @reference_genome_source@ 26 #if str($region).strip() != '':
27 --region '$region'
28 #end if
29 --correctedFile corrected.bam;
28 30
29 31 mv corrected.bam $outFileName;
30 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 32 ]]>
31 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
32 #else:
33 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
34 #end if
35
36 #if str($region).strip() != '':
37 --region '$region'
38 #end if
39
40 #if $advancedOpt.showAdvancedOpt == "yes":
41 --binSize '$advancedOpt.binSize'
42 #end if
43
44 ###set newoutFileName="corrected."+str($outFileFormat)
45 ##--correctedFile $newoutFileName;
46 --correctedFile "corrected.bam";
47
48 ##mv $newoutFileName $outFileName
49 mv "corrected.bam" $outFileName
50 </command> 33 </command>
51 <inputs> 34 <inputs>
52 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> 35 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
53 <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> 36 <param name="bamInput" format="bam" type="data"
37 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted. (--bamfile)" />
54 <expand macro="reference_genome_source" /> 38 <expand macro="reference_genome_source" />
55 <expand macro="effectiveGenomeSize" /> 39 <expand macro="effectiveGenomeSize" />
56
57 <!--
58 <param name="outFileFormat" type="select" label="File format of the output">
59 <option value="bam">bam</option>
60 <option value="bw">bigwig</option>
61 <option value="bg">bedgraph</option>
62 </param>
63 -->
64 <expand macro="region_limit_operation" /> 40 <expand macro="region_limit_operation" />
65
66 <conditional name="advancedOpt">
67 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
68 <option value="no" selected="true">no</option>
69 <option value="yes">yes</option>
70 </param>
71 <when value="no" />
72 <when value="yes">
73 <param name="binSize" type="integer" value="50" min="1"
74 label="Bin size in bp"
75 help="Size of the bins in bp for the output of the bigwig/bedgraph file."/>
76 </when>
77 </conditional>
78 </inputs> 41 </inputs>
79 <outputs> 42 <outputs>
80 <data format="bam" name="outFileName"> 43 <data format="bam" name="outFileName" />
81 <!--<change_format>
82 <when input="outFileFormat" value="bw" format="bigwig" />
83 <when input="outFileFormat" value="bam" format="bam" />
84 <when input="outFileFormat" value="bg" format="bedgraph" />
85 </change_format>-->
86 </data>
87 </outputs> 44 </outputs>
45 <tests>
46 <test>
47 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
48 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
49 <param name="ref_source" value="history" />
50 <param name="input1" value="sequence.2bit" />
51 <param name="effectiveGenomeSize_opt" value="specific" />
52 <param name="effectiveGenomeSize" value="23011544" />
53 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
54 </test>
55 </tests>
88 <help> 56 <help>
89 57 <![CDATA[
90 **What it does** 58 **What it does**
91 59
92 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by 60 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
93 Benjamini and Speed (2012) Nucleic Acids Res. 61 Benjamini and Speed (2012) Nucleic Acids Res.
94 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. 62 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
101 - GC-normalized BAM file 69 - GC-normalized BAM file
102 70
103 ----- 71 -----
104 72
105 @REFERENCES@ 73 @REFERENCES@
106 74 ]]>
107 </help> 75 </help>
108 <expand macro="citations" /> 76 <expand macro="citations" />
109 </tool> 77 </tool>