comparison qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.xml @ 0:8933ecfb6ab2 default tip

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author jiechenable1987
date Fri, 24 Feb 2012 17:42:16 -0500
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1 <tool id="qcma" name="HumMeth27QCReport" version="1.0">
2 <description>Quality Control for a methylation array</description>
3 <command interpreter="python">
4 HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX' -1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path'
5 </command>
6
7 <inputs>
8
9 <param format="tabular" name="inputAVE" type="data" label="Average Beta file"/>
10 <param format="tabular" name="inputCTRL" type="data" label="Control file"/>
11 <param format="tabular" name="inputSAMPLE" type="data" label="Samples Name file"/>
12 <param format="tabular" name="inputDISC" type="data" label="Discarder file" optional="true" />
13
14 <param name="platform" type="select" format="text" label="Type of Illumina Infinium BeadChip methylation array">
15 <option value="Hum27">Infinium HumanMethylation27 BeadChip</option>
16 <option value="Hum450">Infinium HumanMethylation450 BeadChip</option>
17 </param>
18
19 <param name="pval" type="select" format="text" label="p-value threshold number" help="to define which samples keep for the normalization and the following analysis">
20 <option value="0.01">0.01</option>
21 <option value="0.02">0.02</option>
22 <option value="0.03">0.03</option>
23 <option value="0.04">0.04</option>
24 <option value="0.05">0.05</option>
25 <option value="0.06">0.06</option>
26 <option value="0.07">0.07</option>
27 <option value="0.08">0.08</option>
28 <option value="0.09">0.09</option>
29 <option value="0.10">0.10</option>
30 </param>
31
32 <param name="ClustMethod" type="select" format="text" label="Distance measure to be used for clustering">
33 <option value="euclidean">euclidean</option>
34 <option value="maximum">maximum</option>
35 <option value="manhattan">manhattan</option>
36 <option value="canberra">canberra</option>
37 <option value="binary">binary</option>
38 <option value="pearson">pearson</option>
39 <option value="correlation">correlation</option>
40 <option value="spearman">spearman</option>
41 <option value="kendall">kendall</option>
42 </param>
43 <param name="ChrX" type="select" format="text" label="Delete CpGs from chromosome X?">
44 <option value="FALSE">No</option>
45 <option value="TRUE">Yes</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data format="pdf" name="oQualityCheck" label="QualityCheck"/>
50 <data format="pdf" name="oSample" label="Sample"/>
51 <data format="pdf" name="oInternalControl" label="InternalControl"/>
52 <data format="pdf" name="oExplorativeAnalysis" label="ExplorativeAnalysis"/>
53 <data format="text" name="oNormalizedMvalues" label="NormalizedMvalues"/>
54 <data format="xls" name="oQC_Analysis" label="QC_Analysis"/>
55 </outputs>
56
57
58 <help>
59 This tool is a Quality Control for Illumina Infinium methylation arrays. It uses an R package (HumMeth27QCReport) created by
60 Francesco Mancuso and Guglielmo Roma from the Bioinformatics core at the Center for Genomic Regulation in Barcelona.
61 Help: http://biocore.crg.cat/wiki/HumMeth27QCReport and francesco.mancuso@crg.eu
62 </help>
63
64 </tool>