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 |
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| date | Tue, 07 Jun 2011 17:26:58 -0400 |
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| -1:000000000000 | 0:55561a945415 |
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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> |