# HG changeset patch
# User melissacline
# Date 1423701954 28800
# Node ID 1707e82d55bc463c61a957e46c95ebef679f6c17
# Parent  98b498545a52279a9e82639ee457221669f4f36f
Tweaking the parameter labels for the xena import tool

diff -r 98b498545a52 -r 1707e82d55bc xena_import.xml
--- a/xena_import.xml	Wed Jan 14 16:35:12 2015 -0800
+++ b/xena_import.xml	Wed Feb 11 16:45:54 2015 -0800
@@ -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"/>