# HG changeset patch
# User priti
# Date 1401965517 14400
# Node ID 8fe3b46d62b2773f0a9442aa7f0357bf9e8ce7b9
# Parent  506c4cb6d4d75c144b633aad2191ceb9160f7182
Uploaded

diff -r 506c4cb6d4d7 -r 8fe3b46d62b2 test-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc.sample	Thu Jun 05 06:51:57 2014 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 506c4cb6d4d7 -r 8fe3b46d62b2 test-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_data_table_conf.xml.sample	Thu Jun 05 06:51:57 2014 -0400
@@ -0,0 +1,82 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the BFAST mapper format -->
+    <table name="bfast_indexes" comment_char="#">
+        <columns>value, dbkey, formats, name, path</columns>
+        <file path="tool-data/bfast_indexes.loc" />
+    </table>
+    <!-- Locations of nucleotide (mega)blast databases -->
+    <table name="blastdb" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/blastdb.loc" />
+    </table>
+    <!-- Locations of protein (mega)blast databases -->
+    <table name="blastdb_p" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/blastdb_p.loc" />
+    </table>
+    <!-- Locations of indexes in the BWA mapper format -->
+    <table name="bwa_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_index.loc" />
+    </table>
+    <!-- Locations of indexes in the BWA color-space mapper format -->
+    <table name="bwa_indexes_color" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_index_color.loc" />
+    </table>
+    <!-- Locations of MAF files that have been indexed with bx-python -->
+    <table name="indexed_maf_files">
+        <columns>name, value, dbkey, species</columns>
+        <file path="tool-data/maf_index.loc" />
+    </table>
+    <!-- Locations of fasta files appropriate for NGS simulation -->
+    <table name="ngs_sim_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/ngs_sim_fasta.loc" />
+    </table>
+    <!-- Locations of PerM base index files -->
+    <table name="perm_base_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/perm_base_index.loc" />
+    </table>
+    <!-- Locations of PerM color-space index files -->
+    <table name="perm_color_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/perm_color_index.loc" />
+    </table>
+    <!-- Location of Picard dict file and other files -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gatk_sorted_picard_index.loc" />
+    </table>
+    <!-- Available of GATK references -->
+    <table name="gatk_annotations" comment_char="#">
+        <columns>value, name, gatk_value, tools_valid_for</columns>
+        <file path="tool-data/gatk_annotations.txt" />
+    </table>
+    <!-- Location of SRMA dict file and other files -->
+    <table name="srma_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+    <!-- Location of Mosaik files -->
+    <table name="mosaik_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/mosaik_index.loc" />
+    </table>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 506c4cb6d4d7 -r 8fe3b46d62b2 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 05 06:51:57 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    	<package name="vdt" version="0.6">
+        <repository changeset_revision="819edb523f00" name="vdt_dependency" owner="priti" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>	
+</tool_dependency>
diff -r 506c4cb6d4d7 -r 8fe3b46d62b2 vdt_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vdt_wrapper.xml	Thu Jun 05 06:51:57 2014 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool id="VDT" name="vdt" version="0.6">
+  <requirements>
+      	<requirement type="package" version="0.6">vdt</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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