Mercurial > repos > jjohnson > defuse

changeset 5:87033f379b99

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author Jim Johnson <jj@umn.edu>
date Mon, 07 Jan 2013 12:20:39 -0600
parents ffc5e442c1ca
children 5545ec69acbd
files defuse.xml
diffstat 1 files changed, 17 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/defuse.xml	Fri Jan 04 14:59:03 2013 -0600
+++ b/defuse.xml	Mon Jan 07 12:20:39 2013 -0600
@@ -71,9 +71,24 @@
         <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
       </when>  <!-- history -->
   </conditional>  <!-- refGenomeSource -->
-  <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"/>
+  <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
+         help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
+               but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
   <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
+ <outputs>
+  <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
+  <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
+  <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
+    <filter>keep_output == True</filter>
+  </data>
+  <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
+  <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
+  <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
+  <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
+    <filter>do_get_reads == True</filter>
+  </data>
+ </outputs>
  <configfiles>
   <configfile name="defuse_config">
 #import ast
@@ -584,19 +599,7 @@
 #end if
   </configfile>
  </configfiles>
- <outputs>
-  <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
-  <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
-  <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output">
-    <filter>keep_output == True</filter>
-  </data>
-  <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
-    <filter>do_get_reads == True</filter>
-  </data>
-  <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
-  <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
-  <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
- </outputs>
+
  <tests>
  </tests>
  <help>