# HG changeset patch
# User shirish
# Date 1401775972 14400
# Node ID f09520790c35b434bccce275b6febb29bd1d7cbe
# Parent  4b3130814d921bce7e4a317af24f8e90500b9387
Deleted selected files

diff -r 4b3130814d92 -r f09520790c35 softsearch.xml
--- a/softsearch.xml	Tue Jun 03 01:58:01 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<?xml version="1.0"?>
-<tool id="SoftSearch" name="SoftSearch" version="2.4">
-  <requirements>
-      <requirement type="package" version="2.4">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>
-
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diff -r 4b3130814d92 -r f09520790c35 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 03 01:58:01 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="softsearch" version="2.4">
-        <install version="2">
-            <actions>
-		<action type="download_by_url">wget https://s3-us-west-2.amazonaws.com/mayo-bic-tools/softsearch/Softsearch2.4.tar.gz
-</action>
-		<action type="shell_command">tar xvzf Softsearch2.4.tar.gz</action>
-                <action type="shell_command">cd 2.4/</action>
-                <action type="shell_command">perl ./install.pl --prefix=$PWD</action>
-                <action type="shell_command">export PERL5LIB=$PERL5LIB:$PWD:$PWD/lib</action>
-		<action type="shell_command">perl script/SoftSearch.pl</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        </package>
-</tool_dependency>