diff xena_import.xml @ 18:154a9b440b63

Updated the xena jar to version 14, updated the URL of the Xena pages

--- a/xena_import.xml	Tue Jun 02 14:54:24 2015 -0700
+++ b/xena_import.xml	Tue Jun 02 14:55:55 2015 -0700
@@ -32,8 +32,8 @@
     <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="entry">Enter your own</option>
 	<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"/>
@@ -42,8 +42,8 @@
         <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="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">
@@ -57,6 +57,7 @@
 	        <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>
@@ -72,6 +73,7 @@
 	      <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"/>
@@ -89,6 +91,7 @@
 	        <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>
@@ -104,6 +107,7 @@
 	      <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"/>
@@ -121,6 +125,6 @@
     <data format="txt" name="outfile"/>
   </outputs>
   <help>
-    To Appear soon...
+    To Appear, soon...
   </help>
 </tool>