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comparison correctGCBias.xml @ 39:c6f1a059bc7d

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author bgruening
date Fri, 02 Aug 2013 12:18:55 -0400
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1 <tool id="correctGCBias" name="correctGCBias" version="1.0">
2 <description>
3 </description>
4 <command>
5 correctGCBias
6 --bamfile '$bamInput'
7 --species '$species'
8 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
9
10 #if $source.ref_source=="history":
11 --genome $source.input1
12 #else:
13 --genome "${source.input1_2bit.fields.path}"
14 #end if
15
16 #if $advancedOpt.showAdvancedOpt == "yes":
17 #if str($advancedOpt.region.value) != '':
18 --region '$advancedOpt.region'
19 #end if
20
21 --binSize '$advancedOpt.binSize'
22 #end if
23
24 #set newoutFileName="corrected."+str($outFileFormat)
25
26 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
27
28 </command>
29
30 <inputs>
31
32 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
33
34 <param name="bamInput" format="bam" type="data" label="Input BAM file"
35 help="The BAM file must be sorted and indexed."/>
36
37 <param name="species" type="text" value="" label="Species name abbreviation" />
38
39 <conditional name="source">
40 <param name="ref_source" type="select" label="Reference genome">
41 <option value="cached">locally cached</option>
42 <option value="history">in your history</option>
43 </param>
44 <when value="cached">
45 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
46 <options from_data_table="lastz_seqs" />
47 </param>
48 </when>
49 <when value="history">
50 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
51 </when>
52 </conditional>
53
54 <param name="outFileFormat" type="select" label="File format of the output">
55 <option value="bam">bam</option>
56 <option value="bw">bigwig</option>
57 <option value="bg">bedgraph</option>
58 </param>
59
60 <conditional name="advancedOpt">
61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
62 <option value="no" selected="true">no</option>
63 <option value="yes">yes</option>
64 </param>
65 <when value="no" />
66 <when value="yes">
67 <param name="region" type="text" value=""
68 label="Region of the genome to limit the operation to"
69 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
70
71 <param name="binSize" type="integer" value="50" min="1"
72 label="Bin size in bp"
73 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
74 </when>
75 </conditional>
76 </inputs>
77
78 <outputs>
79 <data format="bam" name="outFileName">
80 <change_format>
81 <when input="outFileFormat" value="bw" format="bigwig" />
82 <when input="outFileFormat" value="bam" format="bam" />
83 <when input="outFileFormat" value="bg" format="bedgraph" />
84 </change_format>
85 </data>
86 </outputs>
87 <help>
88
89 **What it does**
90
91 Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
92 bias can later be used to plot the bias or to correct the bias.
93
94 -----
95
96 .. class:: infomark
97
98 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
99
100 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
101
102
103 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
104 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
105 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
106
107 </help>
108
109 </tool>