# HG changeset patch
# User plus91-technologies-pvt-ltd
# Date 1402137659 14400
# Node ID 0f3f0428fa18cc3e9585e9e10696b177e7b0c146
# Parent  a5064e71fe5a3a90c0b9e5b161a520d86df3dd5a
Deleted selected files

diff -r a5064e71fe5a -r 0f3f0428fa18 softsearch_wrapper.xml
--- a/softsearch_wrapper.xml	Sat Jun 07 03:41:24 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<tool id="Softsearch" name="softsearch" version="0.6">
-  <requirements>
-      	<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 | 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 | 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>