diff haplotype_caller.xml @ 13:da03516b528c draft

Fix output filters

--- a/haplotype_caller.xml	Thu Nov 08 10:55:32 2012 -0600
+++ b/haplotype_caller.xml	Thu Nov 08 11:50:01 2012 -0600
@@ -522,7 +522,7 @@
         <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph  File to which debug assembly graph information should be written"/>
         <param name="group" type="text" optional="true" label="group" help="--group / -G  One or more classes/groups of annotations to apply to variant calls"/>
         <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets  Heterozygosity value used to compute prior likelihoods for any locus"/>
-        <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning  The minimum allowed pruning factor in assembly graph. Paths with <= X supporting kmers are pruned from the graph">
+        <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning  The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
             <validator type="in_range" message="value between 0 and 127" min="0" max="127"/>
         </param>
         <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode  Specifies which type of calls we should output">
@@ -551,15 +551,15 @@
         </param>
 
       </when>
-    <plotypes are evaluated using an affine gap penalty Pair HMM./conditional>
+    </conditional>
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
     <data format="vcf" name="graph_out" label="${tool.name} on ${on_string} graph" >
-      <filter>analysis_param_type['graphOutput'] == True</filter>
+      <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['graphOutput'] == True</filter>
     </data>
     <data format="vcf" name="active_region_out" label="${tool.name} on ${on_string} activeRegion" >
-      <filter>analysis_param_type['activeRegionOut'] == True</filter>
+      <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['activeRegionOut'] == True</filter>
     </data>
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
   </outputs>