changeset 0:679f610562de draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/manta.xml	Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,61 @@
+<tool id="manta" name="Manta" version="0.29.6">
+	<description>
+	   SV Caller
+	</description>
+  <requirements>
+    <requirement type="package" version="0.29.6">manta</requirement>
+  </requirements>
+  <command>
+
+		<!-- Linking BAM Indexs to current working directory -->
+    ln -s $normal normal.bam;
+    ln -s $normal.metadata.bam_index normal.bam.bai;
+    ln -s $tumour tumour.bam;
+    ln -s $tumour.metadata.bam_index tumour.bam.bai;
+
+    <!-- Index Reference if from History -->
+    #if $reference_source.reference_source_selector == "history":
+        ln -s $reference_source.ref_file ref.fa;
+        samtools faidx ref.fa;
+    #end if
+
+    python \$MANTA_INSTALL_DIR/install/bin/configManta.py
+      --normalBam=normal.bam
+      --tumorBam=tumour.bam
+      #if $reference_source.reference_source_selector == "history":
+        --referenceFasta=ref.fa
+      #else
+        --referenceFasta=${reference_source.ref_file.fields.path}
+      #end if
+      --runDir=./output;
+
+    ./output/runWorkflow.py 
+      -m local
+      -j \${GALAXY_SLOTS:-1}
+      --quiet;
+
+    gunzip -c ./output/results/variants/somaticSV.vcf.gz > $output;
+
+	</command>
+	<inputs>
+    <conditional name="reference_source">
+      <param label="Choose the source for the reference files" name="reference_source_selector" type="select">
+        <option value="cached">Locally Cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <param label="Genome" name="ref_file" type="select">
+          <options from_data_table="fasta_indexes"/>
+        </param>
+      </when>
+      <when value="history">
+        <param label="Genome" name="ref_file" type="data" format="fasta"/>
+      </when>
+    </conditional>
+    <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
+    <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>   
+  </inputs>
+	<outputs>
+		<data format="vcf" name="output"/>
+	</outputs>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool-data/all_fasta.loc.sample	Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>      <dbkey> <display_name>  <file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3        apiMel3 Honeybee (Apis mellifera): apiMel3      /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /path/to/genome/hg19/hg19canon.fa
+#hg19full       hg19    Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool_data_table_conf.xml.sample	Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc"/>
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool_dependencies.xml	Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="manta" version="0.29.6">
+    <repository changeset_revision="a735b0a388ab" name="package_manta_0_29_6" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>