--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/softsearch_wrapper.xml	Sat Jun 07 05:59:04 2014 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<tool id="Softsearch" name="softsearch" version="0.6">
+  <requirements>
+	<requirement type="set_environment">R_SCRIPT_PATH</requirement>
+      	<requirement type="package" version="0.6">softsearch</requirement>
+  </requirements>
+  <description>for structure variation</description>
+  <command>#if $source.index_source=="history" 
+	        samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | \$R_SCRIPT_PATH/softsearch_wrapper.softsearch SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
+	    #else
+		samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | \$R_SCRIPT_PATH/softsearch_wrapper.softsearch SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
+	    #end if		
+ </command>
+  <inputs>
+      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
+	 <conditional name="source">
+            <param name="index_source" type="select" label="Choose the source for the reference list">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="history">
+                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
+            </when>
+            <when value="cached">
+                  <param name="ref_fasta" type="select" >
+                    <options from_data_table="fasta_indexes">
+                    <validator type="no_options" message="No Fasta file is available" />
+                    </options>
+                  </param>
+            </when>
+        </conditional>
+      <param name="inc" type="hidden" value="n=$RANDOM" />
+     	<param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
+        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> 	
+	<param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
+	<param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
+	<param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
+  </inputs>
+  <outputs>
+      <data format="vcf" name="out_file1" />
+  </outputs>
+  <help>
+  </help>
+</tool>
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