Mercurial > repos > andreu > qcma
comparison HumMeth27QCReport/HumMeth27QCReport.xml~ @ 0:55561a945415 default tip
Migrated tool version 1.0 from old tool shed archive to new tool shed repository
author | andreu |
---|---|
date | Tue, 07 Jun 2011 17:26:58 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:55561a945415 |
---|---|
1 <tool id="qcma" name="HumMeth27QCReport"> | |
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> |