view xena_import.xml @ 3:98b498545a52

Fixed xena_delete to delete the files from the Xena files directory as well as from the database

<tool id="xenaImport" description="Import into XENA from Galaxy" name="XENA Import" version="0.0.1">
  <description>Import from Galaxy into the Xena VM</description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    xena_import.py ${xenaInputData} $outfile 
    #if $source.metadataSource == "json"
        --json ${source.xenaMetadata}
    #else
        --cohort "${source.cohort}" --type ${source.format.metadataType}
        #if $source.format.metadataType == "genomicMatrix" or $source.format.metadataType == "clinicalMatrix":
            #if $source.format.isCustom.dataSubType == "custom"
                #if $source.format.isCustom.customSubType
                    --dataSubType "${source.format.isCustom.customSubType}"
               #end if
            #else
                --dataSubType "${source.format.isCustom.dataSubType}"
            #end if
        #end if
        #if $source.label
            --label "${source.label}"
        #else
            --label  "${xenaInputData.name}"
        #end if
    #end if
    #if $colNormalization:
        --colNormalization 1
    #end if
  </command>
  <inputs>
    <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
    <conditional name="source">
      <param type="select" name="metadataSource" label="Metadata entry">
	<option value="json">Specify json metadata file</option>
	<option value="entry">Enter your own</option>
      </param>
      <when value="json">
          <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/>
      </when>
      <when value="entry">
        <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
        <conditional name="format">
          <param type="select" name="metadataType" label="File Format">
	    <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples)</option>
	    <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers)</option>
	    <option value="mutationVector">Mutation By Position</option>
          </param>
          <when value="genomicMatrix">
	    <conditional name="isCustom">
	      <param type="select" name="dataSubType" label="Type of data">
	        <option value="custom">Enter your own</option>
	        <option value="phenotype">phenotype</option>
	        <option value="copy number">copy number</option>
	        <option value="DNA methylation">DNA methylation</option>
	        <option value="exon expression">exon expression</option>
	        <option value="gene expression">gene expression</option>
	        <option value="gene expression RNAseq">gene expression RNAseq</option>
	        <option value="gene expression Array">gene expression Array</option>
	        <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
	        <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
	        <option value="protein expression RPPA">protein expression RPPA</option>
	        <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
	      </param>
	      <when value="custom">
	        <param type="text" name="customSubType" label="Type of data" optional="true"/>
	      </when>
	      <when value="phenotype"/>
	      <when value="copy number"/>
	      <when value="DNA methylation"/>
	      <when value="exon expression"/>
	      <when value="gene expression"/>
	      <when value="gene expression RNAseq"/>
	      <when value="gene expression Array"/>
	      <when value="somatic mutation (SNP and small INDELs)"/>
	      <when value="somatic mutation (gene level)"/>
	      <when value="protein expression RPPA"/>
	      <when value="PARADIGM pathway activity"/>
	    </conditional>
          </when>
          <when value="clinicalMatrix">
	    <conditional name="isCustom">
	      <param type="select" name="dataSubType" label="Type of data">
	        <option value="custom">Enter your own</option>
	        <option value="phenotype">phenotype</option>
	        <option value="copy number">copy number</option>
	        <option value="DNA methylation">DNA methylation</option>
	        <option value="exon expression">exon expression</option>
	        <option value="gene expression">gene expression</option>
	        <option value="gene expression RNAseq">gene expression RNAseq</option>
	        <option value="gene expression Array">gene expression Array</option>
	        <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
	        <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
	        <option value="protein expression RPPA">protein expression RPPA</option>
	        <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
	      </param>
	      <when value="custom">
	        <param type="text" name="customSubType" label="Type of data" optional="true"/>
	      </when>
	      <when value="phenotype"/>
	      <when value="copy number"/>
	      <when value="DNA methylation"/>
	      <when value="exon expression"/>
	      <when value="gene expression"/>
	      <when value="gene expression RNAseq"/>
	      <when value="gene expression Array"/>
	      <when value="somatic mutation (SNP and small INDELs)"/>
	      <when value="somatic mutation (gene level)"/>
	      <when value="protein expression RPPA"/>
	      <when value="PARADIGM pathway activity"/>
	    </conditional>
          </when>
          <when value="mutationVector"/>
        </conditional>
        <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
      </when>
    </conditional>
    <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/>
  </inputs>
  <outputs>
    <data format="txt" name="outfile"/>
  </outputs>
  <help>
    To Appear soon...
  </help>
</tool>