# HG changeset patch
# User boris
# Date 1335282304 14400
# Node ID db73de0bc05b55c3d8bdb75168258047856350ca
# Parent  20e1957ed95a0f2953b897d06368fd5141225afa
Updated config tool xml -- Fixes tool shed visualization issue

diff -r 20e1957ed95a -r db73de0bc05b MDtag_filter.xml
--- a/MDtag_filter.xml	Fri Apr 20 16:36:41 2012 -0400
+++ b/MDtag_filter.xml	Tue Apr 24 11:45:04 2012 -0400
@@ -1,27 +1,16 @@
 <tool id="MDtag_filter" name="Filter mapped reads" version="1.0.2">
   <description>on MD tag string</description>
-  <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam ${create.choice} $discarded_sam</command>
+  <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam $saveDiscarded $discarded_sam</command>
   <inputs>
     <param format="sam" name="in_sam" type="data" label="Input SAM file"/>
     <param name="n" type="integer" value='0' label="5' end window (n)" help="Any number of mismatches within this window will cause the read to be discarded"/>
     <param name="m" type="integer" value='0' label="3' end window (m)" help="Any number of mismatches within this window will cause the read to be discarded"/>
-    <conditional name="create">
-      <param name="choice" type="select" label="Create additional SAM file for discarded reads?">
-	<option value="no" selected="true">No</option>
-	<option value="yes">Yes</option>
-      </param>
-      <when value="no">
-      <!-- do nothing here -->
-      </when>
-      <when value="yes">
-      <!-- do nothing here -->
-      </when>
-    </conditional>
+    <param name="saveDiscarded" label="Save discarded reads in additional SAM file?" type="boolean" truevalue="yes" falsevalue="no" checked="False"/>
   </inputs>
   <outputs>
     <data format="sam" name="out_sam" label="MDtag_filter_(selected)_from_${in_sam.name}" metadata_source="in_sam"/>
     <data format="sam" name="discarded_sam" label="MDtag_filter_(discarded)_from_${in_sam.name}" metadata_source="in_sam">
-      <filter> (create['choice']=='yes') </filter>
+      <filter> saveDiscarded is True </filter>
     </data>  
   </outputs>
   <tests>
@@ -35,7 +24,7 @@
       <param name="in_sam" value="test_for_md_filter.sam"/>
       <param name="n" value="5"/>
       <param name="m" value="5"/>
-      <param name="choice" value="yes"/>
+      <param name="saveDiscarded" value="yes"/>
       <output name="out_sam" file="test_md_selected.sam"/>
       <output name="discarded_sam" file="test_md_discarded.sam"/>
     </test>