view xena_import.xml @ 54:3e64e6ed5925

update to version 17 step 1, remove xena.jar

<tool id="xenaImport" name="XENA Import" version="0.0.1">
  <description>Load a Galaxy dataset into the Xena Server running on this galaxy instance</description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    xena_import.py ${xenaInputData} $outfile 
    --cohort "${cohort}" --type ${format.metadataType}
    #if $format.metadataType == "genomicMatrix" or $format.metadataType == "clinicalMatrix":
        #if $format.isCustom.dataSubType == "custom"
            #if $format.isCustom.customSubType
                --dataSubType "${format.isCustom.customSubType}"
            #end if
        #else
            --dataSubType "${format.isCustom.dataSubType}"
        #end if
    #end if
    
    #if $label
        --label "${label}"
    #else
        --label "${xenaInputData.name}"
    #end if

    #if $format.metadataType == "genomicMatrix" and $format.withProbeMap.probeMap =="select"
        --probeMap "${format.withProbeMap.probeMapFile}"
    #end if

    #if $format.metadataType == "genomicMatrix" and $format.colNormalization:
        --colNormalization 1
    #end if

    #if $format.metadataType == "mutationVector" and $format.assembly:
        --assembly "${format.assembly}"
    #end if

  </command>
  <inputs>
    <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
    <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) (often genomic data)</option>
	<option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option>
	<option value="mutationVector">Mutation By Position</option>
      </param>
      <when value="genomicMatrix">
	<conditional name="withProbeMap">
	  <param type="select" name="probeMap" label="Identifier to Gene Mapping">
	    <option value="none">No id to gene mapping file</option>
	    <option value="select">Select a id to gene mapping file</option>
	  </param>
	  <when value="none"/>
	  <when value="select">
	    <param type="data" format="tabular" multiple="false" name="probeMapFile" optional="false"/>
	  </when>
        </conditional>

	<conditional name="isCustom">
	  <param type="select" name="dataSubType" label="Type of data">
	    <option value="custom">Enter your own</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="mRNA expression">mRNA expression</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="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="mRNA expression"/>
	  <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>
	
	<param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/>    
      </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>
	  </param>
	  <when value="custom">
	    <param type="text" name="customSubType" label="Type of data" optional="true"/>
	  </when>
	  <when value="phenotype"/>
	</conditional>
      </when>

      <when value="mutationVector">
	<param type="select" name="assembly"  label ="assembly">
	  <option value = "hg19"> hg19</option>
	</param>
      </when>
    </conditional>
    <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
  </inputs>
  <outputs>
    <data format="txt" name="outfile"/>
  </outputs>
  <help>
    To Appear, soon...
  </help>
</tool>