diff bamedit.xml @ 17:7aede075adad draft

Uploaded

--- a/bamedit.xml	Mon Nov 26 10:17:40 2012 -0500
+++ b/bamedit.xml	Mon Nov 26 10:17:56 2012 -0500
@@ -5,7 +5,7 @@
 -->
 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
   <requirements>
-    <requirement type="package" version="0.1.18">samtools</requirement>
+    <requirement type="package" version="0.1.12">samtools</requirement>
   </requirements>
   <description>Merging, splitting, filtering, and QC of BAM files</description>
   <command interpreter="python">bamedit.py $options_file </command>
@@ -40,23 +40,23 @@
       </when>
     </conditional>
  
-    <param name="output_name" type="text" value="output" size="30" label="Output file name"/>
+    <!--<param name="output_name" type="text" value="output" size="30" label="Output file name"/>-->
   </inputs>
 
   <outputs>
-    <data format="bam" name="bamoutm" label="${output_name.value}">
+    <data format="bam" name="bamoutm" label="${tool.name}: merge on ${on_string}">
 	<filter>input_type['input_type_selector'] == 'merge'</filter>
     </data>
-    <data format="bam" name="bamoutf" label="${output_name.value}">
+    <data format="bam" name="bamoutf" label="${tool.name}: filter on ${on_string}">
 	<filter> input_type['input_type_selector'] == 'filter'</filter>
     </data>
-    <data format="bam" name="bamouts1" label="${output_name.value}_part1">
+    <data format="bam" name="bamouts1" label="${tool.name}: split on ${on_string} (part 1)">
 	<filter>input_type['input_type_selector'] == 'split'</filter>
     </data>
-    <data format="bam" name="bamouts2" label="${output_name.value}_part2">
+    <data format="bam" name="bamouts2" label="${tool.name}: split on ${on_string} (part2)">
 	<filter>input_type['input_type_selector'] == 'split'</filter>
     </data>
-    <data format="txt" name="bamoutp" label="${output_name.value}">
+    <data format="txt" name="bamoutp" label="${tool.name}: pileup on ${on_string}">
 	<filter>input_type['input_type_selector'] == 'pileup'</filter>
     </data>
   </outputs>