# HG changeset patch
# User jjohnson
# Date 1548525188 18000
# Node ID c3167ccca38cda75bcb4a31b9ef08245d4d03223
# Parent  bdd93719cededf25aa5ddec37779abb4401c3b41
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit d2317dff5a89016f18038b97d057f47d949e7808-dirty

diff -r bdd93719cede -r c3167ccca38c README
--- a/README	Mon Dec 18 09:31:31 2017 -0500
+++ b/README	Sat Jan 26 12:53:08 2019 -0500
@@ -61,3 +61,9 @@
 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours.
 create_reference_dataset.pl -c config.txt
 
+
+defuse_trinity_analysis.py - Validating deFuse predictions using Trinity de novo assembled transcripts
+
+DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint.  This may be insufficient to predict the effect of the fusion on protein production.  To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint.  The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript.
+
+
diff -r bdd93719cede -r c3167ccca38c create_reference_dataset.xml
--- a/create_reference_dataset.xml	Mon Dec 18 09:31:31 2017 -0500
+++ b/create_reference_dataset.xml	Sat Jan 26 12:53:08 2019 -0500
@@ -164,7 +164,7 @@
 ncbi_prefix = $genome.ncbi_prefix
 
 # Directory where you want your dataset
-dataset_directory = $config_txt.dataset.extra_files_path
+dataset_directory = $config_txt.extra_files_path
 
 #raw
 # Input genome and gene models
@@ -267,7 +267,7 @@
 ## copy config to output
 cp $defuse_config $config_txt
 ## make a data_dir  and ln -s the input fastq
-mkdir -p $config_txt.dataset.extra_files_path
+mkdir -p $config_txt.files_path
 ## create_reference_dataset.pl
 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config 
   </configfile>
diff -r bdd93719cede -r c3167ccca38c defuse.xml
--- a/defuse.xml	Mon Dec 18 09:31:31 2017 -0500
+++ b/defuse.xml	Sat Jan 26 12:53:08 2019 -0500
@@ -62,7 +62,7 @@
         <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
       </param>
       <param name="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries">
-        <option value="no" select="true">no</option>
+        <option value="no" selected="true">no</option>
         <option value="yes">yes</option>
       </param>
       <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
diff -r bdd93719cede -r c3167ccca38c defuse_trinity_analysis.xml
--- a/defuse_trinity_analysis.xml	Mon Dec 18 09:31:31 2017 -0500
+++ b/defuse_trinity_analysis.xml	Sat Jan 26 12:53:08 2019 -0500
@@ -40,19 +40,21 @@
     <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
   </outputs>
   <tests>
-    <test>
-      <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
-      <output name="vcf" file="mm10_results.filtered.vcf"/>
-    </test>
   </tests>
   <help>
 **Defuse Results**
 
 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.   
 
-This program relies on the header line of the results.tsv to determine which columns to use for analysis.   
+DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint.  This may be insufficient to predict the effect of the fusion on protein production.  To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint.  The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript.  
+
+This program relies on the header line of the deFuse results.tsv to determine which columns to use for analysis.   
 
 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
 .. _TrinityRNAseq: http://trinityrnaseq.github.io/
   </help>
+    <expand macro="citations">
+        <citation type="doi">10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/s41598-018-36840-z</citation>
+    </expand>
 </tool>
diff -r bdd93719cede -r c3167ccca38c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 18 09:31:31 2017 -0500
+++ b/tool_dependencies.xml	Sat Jan 26 12:53:08 2019 -0500
@@ -1,27 +1,27 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="defuse" version="0.6.2">
-        <repository changeset_revision="86278e018303" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="86278e018303" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="bowtie" version="1.0.0">
-        <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="gmap" version="2013-05-09">
-        <repository changeset_revision="953f5eb53593" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="953f5eb53593" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="blat" version="35x1">
-        <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="faToTwoBit" version="35x1">
-        <repository changeset_revision="46615329ea72" name="package_fatotwobit_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="46615329ea72" name="package_fatotwobit_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="ada" version="2.0.3">
-        <repository changeset_revision="73f89898eb2a" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="73f89898eb2a" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
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