diff preprocess.xml @ 1:4d25dec9707e

correction

--- a/preprocess.xml	Mon Apr 27 05:48:52 2015 -0400
+++ b/preprocess.xml	Tue Apr 28 11:23:47 2015 +0200
@@ -1,10 +1,7 @@
-<tool id="preprocess" name="Data Normalization" force_history_refresh="True" version="0.1.0">
-   <requirements>
-    <requirement type="set_environment">R_SCRIPT_PATH</requirement>
-    <requirement type="package" version="1.1.2">mpagenomics</requirement>
-   </requirements>
+<tool id="preprocess2" name="Data Normalization" force_history_refresh="True" version="0.1.0">
+  
 	<command interpreter="python">
-    preprocess.py 
+    preprocess2.py 
 		-s '$summary' 
 		-p '$__new_file_path__'  
 		-c '$inputcdffull.name' 
@@ -13,8 +10,9 @@
 		-a '$inputacs.name' 
 		-d '$inputcdffull' 
 		-v '$inputufl' 
-		-h '$inputugp' 
-		-b '$inputacs' 
+		-w '$inputugp' 
+		-b '$inputacs'
+		-e 'datasetName'
   	#if $settings.settingsType == "tumor":
   	-t '$tumorcsv' 
   	#end if
@@ -29,10 +27,11 @@
 	 -u '$__user_id__'
 	 #for $input in $inputs
                 -i "${input}"
-				-n "${input.name}
+				-n "${input.name}"
      #end for
   </command>
   <inputs>
+  	<param name="datasetName" type="text" label="Dataset Name"/>
   	<param name="inputs" type="data" format="cel" multiple="True" label="Cel files dataset" help="Cel files dataset previously uploaded with the Multiple File Datasets tool."/>
     <param name="inputcdffull" type="data" format="cdf" label="cdf file" help=".cdf file name must comply with the following format : &lt; chiptype &gt;,&lt; tag &gt;.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf)." />
     <param name="inputufl" type="data" format="ufl" label="ufl file" help=".ufl file name must start with  &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl)."/>
@@ -67,11 +66,11 @@
   	     variable outputs require a primary dataset. If hidden refresh 
   	     doesn't occur. 
   	-->
-    <data format="dsf" name="summary" label="Dataset summary file of ${input.name} " />
-    <data format="zip" name="zipfigures" label="figures of normalization of ${input.name}">
+    <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
+    <data format="zip" name="zipfigures" label="figures of normalization of ${datasetName}">
     	<filter>outputgraph == "TRUE"</filter>	
     </data>    
-    <data format="log" name="log" label="log of normalization of ${input.name}">
+    <data format="log" name="log" label="log of normalization ${datasetName}">
     	<filter>outputlog == "TRUE"</filter>
     </data>
   </outputs>