--- a/deletion_predictor.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/deletion_predictor.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.2">
+<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.3">
   <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description>
   <macros>
     <import>toolshed_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements" />
   <version_command>python3 -m MiModD version -q</version_command>
   <command>
     python3 -m MiModD delcall
@@ -15,18 +15,18 @@
   </command>
 
   <inputs>
-    <repeat name="list_input" title="Aligned reads input source" default="1" min="1">
-        <param name="bamfile" type="data" format="bam" label="input BAM file" />
+    <repeat default="1" min="1" name="list_input" title="Aligned reads input source">
+        <param format="bam" label="input BAM file" name="bamfile" type="data" />
     </repeat>
-    <param name="covfile" type="data" format="bcf" label="BCF variant call file to extract coverage from" help="Use the Variant Calling tool to generate this file."/>
-    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." />
-    <param name="include_uncovered" type="boolean" label="include low-coverage regions" truevalue="-u" falsevalue="" checked="false" help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." />  
-    <param name="max_cov" type="integer" value="0" label="maximal coverage allowed inside a low-coverage region (default: 0)" help="The maximal coverage at a site allowed to consider it as part of a low-coverage region" />
-    <param name="min_size" type="integer" value="100" label="minimal deletion size (default: 100)" help="A low-coverage region must consist of at least this number of consecutive bases below the maximal coverage to consider it in further analyses."/>
+    <param format="bcf" help="Use the Variant Calling tool to generate this file." label="BCF variant call file to extract coverage from" name="covfile" type="data" />
+    <param checked="false" falsevalue="" help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." label="group reads based on read group id only" name="group_by_id" truevalue="-i" type="boolean" />
+    <param checked="false" falsevalue="" help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." label="include low-coverage regions" name="include_uncovered" truevalue="-u" type="boolean" />  
+    <param help="The maximal coverage at a site allowed to consider it as part of a low-coverage region" label="maximal coverage allowed inside a low-coverage region (default: 0)" name="max_cov" type="integer" value="0" />
+    <param help="A low-coverage region must consist of at least this number of consecutive bases below the maximal coverage to consider it in further analyses." label="minimal deletion size (default: 100)" name="min_size" type="integer" value="100" />
   </inputs>
 
   <outputs>
-    <data name="outputfile" format="gff" />
+    <data format="gff" name="outputfile" />
   </outputs>
 
 <help>
@@ -62,4 +62,4 @@
 
 </help>
 
-</tool>
+</tool>
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