# HG changeset patch
# User jjohnson
# Date 1451940900 18000
# Node ID 225750bf37704bab156909c705d22cced65c4e17
# Parent  ed07bcc39f6eda216945269a883a2712fa516193
Uploaded

diff -r ed07bcc39f6e -r 225750bf3770 README
--- a/README	Wed May 06 14:31:57 2015 -0500
+++ b/README	Mon Jan 04 15:55:00 2016 -0500
@@ -1,11 +1,12 @@
-The DeFuse galaxy tool is based on DeFuse_Version_0.6.1
+The DeFuse galaxy tool is based on DeFuse_Version_0.6.2
 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+https://bitbucket.org/dranew/defuse
 
 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
 
 
 Manual:
-http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
+http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2
 
 The included tool_dependencies.xml will download and install the defuse code.  
 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.  
@@ -40,7 +41,7 @@
 
 Galaxy will try to auto-install dependencies:
 
-External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1 )
+External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2 )
 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.
 Download samtools
 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools.
diff -r ed07bcc39f6e -r 225750bf3770 create_reference_dataset.xml
--- a/create_reference_dataset.xml	Wed May 06 14:31:57 2015 -0500
+++ b/create_reference_dataset.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,16 +1,17 @@
-<tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1">
+<tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
  <description>create a defuse reference from Ensembl and UCSC sources</description>
- <requirements>
-  <requirement type="package" version="0.6.1">defuse</requirement>
-  <requirement type="package" version="0.1.18">samtools</requirement>
-  <requirement type="package" version="1.0.0">bowtie</requirement>
-  <requirement type="package" version="2013-05-09">gmap</requirement>
-  <requirement type="package" version="latest">kent</requirement>
- </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+        <expand macro="mapping_requirements" />
+    </requirements>
   <command interpreter="command"> /bin/bash $defuse_script </command>
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -18,6 +19,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -220,6 +235,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
@@ -286,4 +304,5 @@
 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.  
 
  </help>
+    <expand macro="citations"/>
 </tool>
diff -r ed07bcc39f6e -r 225750bf3770 datamanager_create_reference.xml
--- a/datamanager_create_reference.xml	Wed May 06 14:31:57 2015 -0500
+++ b/datamanager_create_reference.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -17,6 +17,7 @@
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -24,6 +25,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -221,6 +236,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
@@ -228,7 +246,7 @@
 remove_job_temp_files                       = yes
 #end raw
   </configfile>
-  <configfile name="defuse_script">
+  <configfile name="defuse_script">#slurp
 #!/bin/bash
 ## define some things for cheetah proccessing
 #set $amp = chr(38)
diff -r ed07bcc39f6e -r 225750bf3770 defuse.xml
--- a/defuse.xml	Wed May 06 14:31:57 2015 -0500
+++ b/defuse.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,12 +1,13 @@
-<tool id="defuse" name="DeFuse" version="1.6.1">
- <description>identify fusion transcripts</description>
- <requirements>
-  <requirement type="package" version="0.6.1">defuse</requirement>
-  <requirement type="package" version="0.1.19">samtools</requirement>
-  <requirement type="package" version="1.0.0">bowtie</requirement>
-  <requirement type="package" version="2013-05-09">gmap</requirement>
-  <requirement type="package" version="latest">kent</requirement>
- </requirements>
+<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1">
+    <description>identify fusion transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+        <expand macro="mapping_requirements" />
+        <expand macro="r_requirements" />
+    </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
   <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
@@ -79,7 +80,7 @@
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
-  <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
+  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
@@ -570,8 +571,10 @@
 cp $defuse_config $config_txt
 ## make a data_dir  and ln -s the input fastq
 mkdir -p data_dir
-ln -s $left_pairendreads data_dir/reads_1.fastq
-ln -s $right_pairendreads data_dir/reads_2.fastq
+## ln -s "$left_pairendreads" data_dir/reads_1.fastq
+## ln -s "$right_pairendreads" data_dir/reads_2.fastq
+cp "$left_pairendreads" data_dir/reads_1.fastq
+cp "$right_pairendreads" data_dir/reads_2.fastq
 ## ln to output_dir in from_work_dir
 #if $defuse_out.__str__ != 'None':
 mkdir -p $defuse_out.dataset.extra_files_path
@@ -580,7 +583,7 @@
 mkdir -p output_dir
 #end if
 ## run defuse.pl
-perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
+perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
@@ -746,4 +749,5 @@
   3596	TGGGGGTTGAGGCTTCTGTTCCCAGGTTCCATGACCTCAGAGGTGGCTGGTGAGGTTATGACCTTTGCCCTCCAGCCCTGGCTTAAAACCTCAGCCCTAGGACCTGGTTAAAGGAAGGGGAGATGGAGCTTTGCCCCGACCCCCCCCCGTTCCCCTCACCTGTCAGCCCGAGCTGGGCCAGGGCCCCTAGGTGGGGAACTGGGCCGGGGGGCGGGCACAAGCGGAGGTGGTGCCCCCAAAAGGGCTCCCGGTGGGGTCTTGCTGAGAAGGTGAGGGGTTCCCGGGGCCGCAGCAGGTGGTGGTGGAGGAGCCAAGCGGCTGTAGAGCAAGGGGTGAGCAGGTTCCAGACCGTAGAGGCGGGCAGCGGCCACGGCCCCGGGTCCAGTTAGCTCCTCACCCGCCTCATAGAAGCGGGGTGGCCTTGCCAGGCGTGGGGGTGCTGCC|TTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCAGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGCCCCCCGGCCGGGGCCGGAGAGGGGCTGACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGCTACTGGCAGG	250	7.00711162298275e-72	0.00912124762512338	0.00684237452309549	N	N	3.31745197152461	3.47233119514066	3.31745197152461	splitr	7	0.0157657657657656	0	0	N	0.0135135135135136	N	N	0	0	ENSG00000156860	ENSG00000212932	-	+	16	21	30682131	48111157	coding	upstream	FBRS	RPL23AP4	30670289	48110676	+	+	0.0157657657657656	30680678	9827473	-	+	Y	-	-	N	output_dir	2	1	1.11111111111111	1	1	1	N	N	0	1	9	0.325530693397641	0.296465452915709	0.325530693397641	0.296465452915709	2	-	-	
 
  </help>
+    <expand macro="citations"/>
 </tool>
diff -r ed07bcc39f6e -r 225750bf3770 defuse_bamfastq.xml
--- a/defuse_bamfastq.xml	Wed May 06 14:31:57 2015 -0500
+++ b/defuse_bamfastq.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
-<tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1">
+<tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1">
   <description>converts a bam file to fastq files.</description>
-  <requirements>
-    <requirement type="package" version="0.6.1">defuse</requirement>
-  </requirements>
-  <version_command>bamfastq --version</version_command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+    </requirements>
   <command>bamfastq
     #if $pair == True :
       $pair
@@ -57,4 +59,5 @@
   <help>
     bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
   </help>
+    <expand macro="citations"/>
 </tool>
diff -r ed07bcc39f6e -r 225750bf3770 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -0,0 +1,28 @@
+<macros>
+    <token name="@DEFUSE_VERSION@">0.6.2</token>
+    <xml name="defuse_requirement">
+            <requirement type="package" version="@DEFUSE_VERSION@">defuse</requirement>
+    </xml>
+    <xml name="mapping_requirements">
+            <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="1.0.0">bowtie</requirement>
+            <requirement type="package" version="2013-05-09">gmap</requirement>
+            <requirement type="package" version="latest">kent</requirement>
+    </xml>
+    <xml name="r_requirements">
+            <requirement type="package" version="3.1.2">R</requirement>
+            <requirement type="package" version="2.0.3">ada</requirement>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+            <exit_code range="1:"  level="fatal" description="Error" />
+        </stdio>
+  </xml>
+  <xml name="citations">
+      <citations>
+        <citation type="doi">10.1371/journal.pcbi.1001138</citation>
+        <yield />
+      </citations>
+  </xml>
+</macros>
diff -r ed07bcc39f6e -r 225750bf3770 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 06 14:31:57 2015 -0500
+++ b/tool_dependencies.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,18 +1,24 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="defuse" version="0.6.1">
-        <repository name="package_defuse_0_6_1" owner="jjohnson" changeset_revision="252b7103d152" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="defuse" version="0.6.2">
+        <repository changeset_revision="bf5636f162fe" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.19">
-        <repository name="package_samtools_0_1_19" owner="iuc"  changeset_revision="632f1a03db92" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.0.0">
-        <repository name="package_bowtie_1_0_0" owner="jjohnson"  changeset_revision="e682af6a72cd" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="gmap" version="2013-05-09">
-        <repository name="package_gmap_2013_05_09" owner="jjohnson"  changeset_revision="8bacc25e2023" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="8bacc25e2023" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="kent" version="latest">
-        <repository name="package_kent" owner="jjohnson"  changeset_revision="822c8d19cfe3" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="822c8d19cfe3" name="package_kent" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="73cd1d529330" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ada" version="2.0.3">
+        <repository changeset_revision="50f0e0825d41" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>