Mercurial > repos > andreu > qcma
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/HumMeth27QCReport/HumMeth27QCReport.xml~ Tue Jun 07 17:26:58 2011 -0400 @@ -0,0 +1,64 @@ +<tool id="qcma" name="HumMeth27QCReport"> + <description>Quality Control for a methylation array</description> + <command interpreter="python"> + 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' + </command> + + <inputs> + + <param format="tabular" name="inputAVE" type="data" label="Average Beta file"/> + <param format="tabular" name="inputCTRL" type="data" label="Control file"/> + <param format="tabular" name="inputSAMPLE" type="data" label="Samples Name file"/> + <param format="tabular" name="inputDISC" type="data" label="Discarder file" optional="true" /> + + <param name="platform" type="select" format="text" label="Type of Illumina Infinium BeadChip methylation array"> + <option value="Hum27">Infinium HumanMethylation27 BeadChip</option> + <option value="Hum450">Infinium HumanMethylation450 BeadChip</option> + </param> + + <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"> + <option value="0.01">0.01</option> + <option value="0.02">0.02</option> + <option value="0.03">0.03</option> + <option value="0.04">0.04</option> + <option value="0.05">0.05</option> + <option value="0.06">0.06</option> + <option value="0.07">0.07</option> + <option value="0.08">0.08</option> + <option value="0.09">0.09</option> + <option value="0.10">0.10</option> + </param> + + <param name="ClustMethod" type="select" format="text" label="Distance measure to be used for clustering"> + <option value="euclidean">euclidean</option> + <option value="maximum">maximum</option> + <option value="manhattan">manhattan</option> + <option value="canberra">canberra</option> + <option value="binary">binary</option> + <option value="pearson">pearson</option> + <option value="correlation">correlation</option> + <option value="spearman">spearman</option> + <option value="kendall">kendall</option> + </param> + <param name="ChrX" type="select" format="text" label="Delete CpGs from chromosome X?"> + <option value="FALSE">No</option> + <option value="TRUE">Yes</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="oQualityCheck" label="QualityCheck"/> + <data format="pdf" name="oSample" label="Sample"/> + <data format="pdf" name="oInternalControl" label="InternalControl"/> + <data format="pdf" name="oExplorativeAnalysis" label="ExplorativeAnalysis"/> + <data format="text" name="oNormalizedMvalues" label="NormalizedMvalues"/> + <data format="xls" name="oQC_Analysis" label="QC_Analysis"/> + </outputs> + + + <help> +This tool is a Quality Control for Illumina Infinium methylation arrays. It uses an R package (HumMeth27QCReport) created by +Francesco Mancuso and Guglielmo Roma from the Bioinformatics core at the Center for Genomic Regulation in Barcelona. +Help: http://biocore.crg.cat/wiki/HumMeth27QCReport and francesco.mancuso@crg.eu + </help> + +</tool>