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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
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55561a945415 Migrated tool version 1.0 from old tool shed archive to new tool shed repository
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1 <tool id="qcma" name="HumMeth27QCReport" version="1.0">
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2 <description>Quality Control for a methylation array</description>
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3 <command interpreter="python">
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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'
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5 </command>
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6
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7 <inputs>
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8
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9 <param format="tabular" name="inputAVE" type="data" label="Average Beta file"/>
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10 <param format="tabular" name="inputCTRL" type="data" label="Control file"/>
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11 <param format="tabular" name="inputSAMPLE" type="data" label="Samples Name file"/>
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12 <param format="tabular" name="inputDISC" type="data" label="Discarder file" optional="true" />
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13
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14 <param name="platform" type="select" format="text" label="Type of Illumina Infinium BeadChip methylation array">
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15 <option value="Hum27">Infinium HumanMethylation27 BeadChip</option>
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16 <option value="Hum450">Infinium HumanMethylation450 BeadChip</option>
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17 </param>
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18
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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">
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20 <option value="0.01">0.01</option>
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21 <option value="0.02">0.02</option>
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22 <option value="0.03">0.03</option>
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23 <option value="0.04">0.04</option>
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24 <option value="0.05">0.05</option>
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25 <option value="0.06">0.06</option>
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26 <option value="0.07">0.07</option>
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27 <option value="0.08">0.08</option>
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28 <option value="0.09">0.09</option>
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29 <option value="0.10">0.10</option>
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30 </param>
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31
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32 <param name="ClustMethod" type="select" format="text" label="Distance measure to be used for clustering">
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33 <option value="euclidean">euclidean</option>
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34 <option value="maximum">maximum</option>
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35 <option value="manhattan">manhattan</option>
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36 <option value="canberra">canberra</option>
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37 <option value="binary">binary</option>
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38 <option value="pearson">pearson</option>
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39 <option value="correlation">correlation</option>
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40 <option value="spearman">spearman</option>
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41 <option value="kendall">kendall</option>
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42 </param>
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43 <param name="ChrX" type="select" format="text" label="Delete CpGs from chromosome X?">
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44 <option value="FALSE">No</option>
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45 <option value="TRUE">Yes</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data format="pdf" name="oQualityCheck" label="QualityCheck"/>
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50 <data format="pdf" name="oSample" label="Sample"/>
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51 <data format="pdf" name="oInternalControl" label="InternalControl"/>
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52 <data format="pdf" name="oExplorativeAnalysis" label="ExplorativeAnalysis"/>
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53 <data format="text" name="oNormalizedMvalues" label="NormalizedMvalues"/>
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54 <data format="xls" name="oQC_Analysis" label="QC_Analysis"/>
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55 </outputs>
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56
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57
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58 <help>
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59 This tool is a Quality Control for Illumina Infinium methylation arrays. It uses an R package (HumMeth27QCReport) created by
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60 Francesco Mancuso and Guglielmo Roma from the Bioinformatics core at the Center for Genomic Regulation in Barcelona.
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61 Help: http://biocore.crg.cat/wiki/HumMeth27QCReport and francesco.mancuso@crg.eu
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62 </help>
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63
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64 </tool>