diff xena_import.xml @ 0:8bb037f88ed2

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import.xml	Tue Jan 13 23:37:23 2015 -0500
@@ -0,0 +1,122 @@
+<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
+  </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>
+  </inputs>
+  <outputs>
+    <data format="txt" name="outfile"/>
+  </outputs>
+  <help>
+    To Appear soon...
+  </help>
+</tool>