# HG changeset patch
# User anton
# Date 1396643274 14400
# Node ID 932378b3f1d9cfc519bd6ab28ffcb6644855cd46
# Parent  24fc171d4bfaeceaf54dbde2ff8746f05654dfd8
Fixes to XML tool definition

diff -r 24fc171d4bfa -r 932378b3f1d9 leftalign.xml
--- a/leftalign.xml	Fri Apr 04 16:09:14 2014 -0400
+++ b/leftalign.xml	Fri Apr 04 16:27:54 2014 -0400
@@ -4,7 +4,7 @@
     <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
-  <description> - leftaligner</description>
+  <description> indels in BAM datasets</description>
   <command>
     ##set up input files
     #set $reference_fasta_filename = "localref.fa"
@@ -32,7 +32,7 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
+            <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align">
               <validator type="unspecified_build" />
               <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
             </param>
@@ -44,7 +44,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
+            <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>