# HG changeset patch
# User gkumar09
# Date 1449032264 18000
# Node ID 887986b43271ebddaf6636d493ec6ef4bbf28a10

Uploaded

diff -r 000000000000 -r 887986b43271 trinityctatfusion/.___add_to_PATH_setting.txt
Binary file trinityctatfusion/.___add_to_PATH_setting.txt has changed
diff -r 000000000000 -r 887986b43271 trinityctatfusion/__add_to_PATH_setting.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/__add_to_PATH_setting.txt	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,1 @@
+/usr/local/bin
diff -r 000000000000 -r 887986b43271 trinityctatfusion/discasm.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/discasm.xml	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,37 @@
+<tool id="discasm" name="DISCASM" version="0.0.1">
+    <description>DISCASM</description>
+    <command>
+     sh discasm_fusion_toolshed_wrapper.sh
+     $bam
+     $chimeric
+     $left_input
+     $right_input
+     "subdir" 
+    </command>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param format="bam" name="bam" type="data" label="Aligned bam" help="Aligned Bam from Star Fusion tool"/>
+      <param format="tabular" name="chimeric" type="data" label="Chimeric.out.junction" help="Chimeric junction from Star Fusion tool"/>
+      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
+      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
+    </inputs>
+    <outputs>
+      <data format="fasta" name="oases.transcripts" label="${tool.name} on ${on_string}: Oasis Transcripts" from_work_dir="subdir/oasesMultiK_out_dir/oases.transcripts.fa" />
+    </outputs>
+    <tests>
+      <test>
+	<param name="Aligned bam" value="Aligned.bam" />
+	<param name="chimeric" value="chimeric.out.junction" />
+        <output name="oases.transcripts" file="oases.transcripts.fa"/>
+      </test>
+    </tests>
+    <help>
+        DISCASM Draft
+    </help>
+</tool>
diff -r 000000000000 -r 887986b43271 trinityctatfusion/discasm_fusion_toolshed_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/discasm_fusion_toolshed_wrapper.sh	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,11 @@
+#!/bin/bash -l
+
+umask 0002
+
+bam=$1
+chimeric=$2
+LEFT_FQ=$3
+RIGHT_FQ=$4
+OUTPUTDIR=$5
+
+$DISCASM_DIR/DISCASM --aligned_bam $bam --chimeric_junctions $chimeric --left_fq $LEFT_FQ --right_fq $RIGHT_FQ --denovo_assembler OasesMultiK --out_dir $OUTPUTDIR 
diff -r 000000000000 -r 887986b43271 trinityctatfusion/fusion_annotator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/fusion_annotator.xml	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,27 @@
+<tool id="fusion_annotator" name="fusion_annotator" version="0.0.1">
+    <description>Fusion-Annotator</description>
+    <command>
+    sh fusion_annotator_toolshed_wrapper.sh
+    $fusion_candidate 
+    </command>
+    <macros>
+    </macros>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param name="fusion_candidate" type="data" label="Fusion Candidate List:" help=""/>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="annotation_list" label="${tool.name} on ${on_string}: annotation" from_work_dir="annotation.txt"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        fusion annotator
+    </help>
+</tool>
diff -r 000000000000 -r 887986b43271 trinityctatfusion/fusion_annotator_toolshed_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/fusion_annotator_toolshed_wrapper.sh	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,10 @@
+#!/bin/bash -l
+
+umask 0002
+
+. /broad/software/scripts/useuse
+
+fusion_file=$1
+
+$FUSION_ANNOTATOR/FusionAnnotator --fusion_annot_lib $FUSION_ANNOTATOR/Hg19_CTAT_fusion_annotator_lib --annotate $fusion_file >> annotation.txt
+
diff -r 000000000000 -r 887986b43271 trinityctatfusion/fusion_inspector_new.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/fusion_inspector_new.xml	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,70 @@
+<tool id="fusion-inspector-new" name="Fusion-Inspector-new" version="0.0.3">
+    <description>Fusion Inspector</description>
+    <command>
+    sh fusion_inspector_toolshed_wrapper.sh
+    $fusion_candidates_list
+    $left_input
+    $right_input
+    "subdir"
+    $method 
+    $trinity_status.trinity
+    </command>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/>
+      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>      
+      <param name="method" type="select" label="Choose method:">
+             <option value="HISAT">HISAT</option>
+             <option value="STAR">STAR</option>
+             <option value="GSNAP">GSNAP</option>
+      </param>
+      <conditional name="trinity_status">
+           <param name="trinity" type="select" label="Use Trinity:">
+             <option value="true">True</option>
+             <option value="false">False</option>
+           </param>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data format="text" name="finsepector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/>
+      <data format="text" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/>
+      <data format="fasta" name="finspector_fa" label="finspector_fasta" from_work_dir="subdir/finspector.fa"/>
+      <data format="bed" name="finspector_bed" label="finspector_bed" from_work_dir="subdir/finspector.bed"/>
+      <data format="tabular" name="FusionJuncSpan" label="FusionJuncSpan" from_work_dir="subdir/finspector.igv.FusionJuncSpan"/>
+      <data format="bed" name="junction_bed" label="junction_bed" from_work_dir="subdir/finspector.junction_reads.bam.bed"/>
+      <data format="bam" name="junction_bam" label="junction_bam" from_work_dir="subdir/finspector.junction_reads.bam"/>
+      <data format="bam" name="spanning_bam" label="spanning_bam" from_work_dir="subdir/finspector.spanning_reads.bam"/>
+      <data format="bed" name="spanning_bed" label="spanning_bed" from_work_dir="subdir/finspector.spanning_reads.bam.bed"/>
+      <data format="bed" name="trinity_bed" label="trinity_bed" from_work_dir="subdir/finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed">
+            <filter>trinity_status['trinity'] == "true"</filter>
+      </data>
+      <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/fusion_inspector_web.json"/>
+    </outputs>
+    <tests>
+      <test>
+	<param name="fusion listA" value="listA.txt" />
+	<param name="fusion listB" value="listB.txt" />
+	<param name="LeftFastq" value="left.fq" />
+	<param name="RightFastq" value="right.fq" />
+	<output name="finsepector_idx" file="finspector.fa.fai" />
+	<output name="cytoband" file="cytoband.txt" />
+	<output name="finsepector_bed" file="finspector.bed" />
+	<output name="junction_bed" file="finspector.junction_reads.bam.bed" />
+	<output name="finsepector_fasta" file="finspector.fa" />
+	<output name="junction_bam" file="junction_reads.bam" />
+	<output name="spanning_bam" file="spanning_reads.bam" />
+	<output name="spanning_bed" file="spanning_reads.bam.bed" />
+	<output name="trinity_bed" file="trinity.gff3.bed.sorted.bed" />
+      </test>
+    </tests>
+    <help>
+       Fusion Inspector New
+    </help>
+</tool>
diff -r 000000000000 -r 887986b43271 trinityctatfusion/fusion_inspector_toolshed_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/fusion_inspector_toolshed_wrapper.sh	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,28 @@
+#!/bin/bash -l
+
+umask 0002
+
+. /broad/software/scripts/useuse
+
+reuse .samtools-0.1.19
+
+fusions_list=$1
+LEFT_FQ=$2
+RIGHT_FQ=$3
+OUTPUTDIR=$4
+method=$5
+trinity=$6
+
+cmd="$FUSION_DIR/FusionInspector --fusions $fusions_list --genome_lib $CTAT_GENOME_LIB --left_fq $LEFT_FQ --right $RIGHT_FQ --out_dir $OUTPUTDIR --out_prefix "finspector" --prep_for_IGV --align_utils $method" 
+
+trinity_f=" --include_Trinity"
+
+if [ $trinity = "true" ] 
+then
+combined_cmd=$cmd$trinity_f
+$combined_cmd
+else
+$cmd
+fi
+
+##echo $bsub 
diff -r 000000000000 -r 887986b43271 trinityctatfusion/gmap_fusion.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/gmap_fusion.xml	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,40 @@
+<tool id="gmap_fusion" name="GMAP-fusion" version="0.0.1">
+    <description>GMAP-fusion</description>
+    <command>
+    sh gmap_fusion_toolshed_wrapper.sh
+    $discasm_trans
+    $left_input
+    $right_input
+    "subdir" 
+    </command>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param format="fasta" name="discasm_trans" type="data" label="Discasm Transcript" help="Discasm generated transcript fasta"/>
+      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
+      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="discasm_trans" value="discasm_trans.fasta" />
+        <param name="left_input" value="left.fq" />
+	<param name="right_input" value="right.fq" />
+        <output name="gmapfusion" file="GMAP-fusion.final"/>
+      </test>
+    </tests>
+
+
+
+
+    <help>
+        GMAP-fusion 
+    </help>
+</tool>
diff -r 000000000000 -r 887986b43271 trinityctatfusion/gmap_fusion_toolshed_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/gmap_fusion_toolshed_wrapper.sh	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,10 @@
+#!/bin/bash -l
+
+umask 0002
+
+discasm_trans=$1
+LEFT_FQ=$2
+RIGHT_FQ=$3
+OUTPUTDIR=$4
+
+$GMAP_FUSION_DIR/GMAP-fusion -T $discasm_trans --left_fq $LEFT_FQ --right_fq $RIGHT_FQ --genome_lib_dir $CTAT_GENOME_LIB --output $OUTPUTDIR 
diff -r 000000000000 -r 887986b43271 trinityctatfusion/star_fusion_new.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/star_fusion_new.xml	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,39 @@
+<tool id="star-fusion-new" name="Star-fusion-new" version="0.0.2">
+    <description>Fusion-finding Pipeline using the STAR aligner</description>
+    <command>
+    sh star_fusion_toolshed_wrapper.sh
+    $left_input
+    $right_input
+    "subdir" 
+    </command>
+    <macros>
+    </macros>
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    <inputs>
+      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+    </inputs>
+    <outputs>
+      <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
+      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/Aligned.sortedByCoord.out.bam"/>
+      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_candidates.final.abridged"/>
+      <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/Chimeric.out.junction"/> 
+    </outputs>
+    <tests>
+      <test>
+        <param name="left_input" value="left.fq" />
+	<param name="right_input" value="right.fq" />
+        <output name="aligned_bam" file="Aligned.out.bam"/>
+	<output name="chimeric_junction" file="chimeric.out.junction"/>
+      </test>
+    </tests>
+    <help>
+        STAR-fusion New
+    </help>
+</tool>
diff -r 000000000000 -r 887986b43271 trinityctatfusion/star_fusion_toolshed_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityctatfusion/star_fusion_toolshed_wrapper.sh	Tue Dec 01 23:57:44 2015 -0500
@@ -0,0 +1,12 @@
+#!/bin/bash -l
+
+umask 0002
+
+
+LEFT_FQ=$1
+RIGHT_FQ=$2
+OUTPUTDIR=$3
+
+GENOME_LIB=$CTAT_GENOME_LIB
+
+$STAR_FUSION_DIR/STAR-Fusion --genome_lib_dir $GENOME_LIB --left_fq $LEFT_FQ --right_fq $RIGHT_FQ --output_dir $OUTPUTDIR