view HumMeth27QCReport/HumMeth27QCReport.xml~ @ 0:1d2730e6bb39 default tip

Migrated tool version 1.0 from old tool shed archive to new tool shed repository

<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 [e-mail]
  </help>

</tool>