# HG changeset patch
# User devteam
# Date 1444754035 14400
# Node ID 3279e193b966e818d5d08781d45d67e17ca72287
# Parent  ae4ed992d98a015937bb327c660c9f7830f5ff7c
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r ae4ed992d98a -r 3279e193b966 tool-data/bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample	Tue Oct 13 12:33:55 2015 -0400
@@ -0,0 +1,37 @@
+# bowtie_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie and Tophat.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+#    /depot/data2/galaxy/hg19/bowtie/
+#
+# containing hg19 genome and hg19.*.ewbt files, such as:
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.ewbt
+#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.ewbt
+#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.ewbt
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19	hg19	Human (hg19)	/depot/data2/galaxy/hg19/bowtie/hg19canon
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/mm10/bowtie/mm10
+#dm3	dm3	      D. melanogaster (dm3)	/depot/data2/galaxy/mm10/bowtie/dm3
+#
+#
diff -r ae4ed992d98a -r 3279e193b966 tool-data/tophat_fusion_blastdb.loc.sample
--- a/tool-data/tophat_fusion_blastdb.loc.sample	Mon Jan 27 13:11:25 2014 -0500
+++ b/tool-data/tophat_fusion_blastdb.loc.sample	Tue Oct 13 12:33:55 2015 -0400
@@ -1,37 +1,13 @@
 #This is a sample file distributed with Galaxy that is used to define a
-#list of nucleotide BLAST databases, using three columns tab separated
+#list of nucleotide BLAST databases for tophat-fusion-post, using fod columns tab separated
 #(longer whitespace are TAB characters):
 #
-#<unique_id>	<database_caption>	<base_name_path>
-#
-#The captions typically contain spaces and might end with the build date.
-#It is important that the actual database name does not have a space in
-#it, and that there are only two tabs on each line.
-#
-#So, for example, if your database is nt and the path to your base name 
-#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry 
-#would look like this:
-#
-#nt_02_Dec_2009      nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
+#<unique_id>	<dbkey>	<name>	<path>
 #
-#and your /depot/data2/galaxy/blastdb/nt directory would contain all of 
-#your "base names" (e.g.):
-#
-#-rw-r--r--  1 wychung galaxy  23437408 2008-04-09 11:26 nt.chunk.00.nhr
-#-rw-r--r--  1 wychung galaxy   3689920 2008-04-09 11:26 nt.chunk.00.nin
-#-rw-r--r--  1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
-#...etc...
+# For example:
 #
-#Your blastdb.loc file should include an entry per line for each "base name" 
-#you have stored.  For example:
-#
-#nt_02_Dec_2009		nt 02 Dec 2009		/depot/data2/galaxy/blastdb/nt/nt.chunk
-#wgs_30_Nov_2009	wgs 30 Nov 2009	/depot/data2/galaxy/blastdb/wgs/wgs.chunk
-#test_20_Sep_2008	test 20 Sep 2008	/depot/data2/galaxy/blastdb/test/test
-#...etc...
+# hg19	hg19	hg19-blast	/depot/data2/galaxy/hg19/blastdb/
 #
 #You can download the NCBI provided protein databases like NT from here:
 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
-#
-#See also blastdb_p.loc which is for any protein BLAST database, and
-#blastdb_d.loc which is for any protein domains databases (like CDD).
\ No newline at end of file
+#
\ No newline at end of file
diff -r ae4ed992d98a -r 3279e193b966 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Jan 27 13:11:25 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Tue Oct 13 12:33:55 2015 -0400
@@ -1,7 +1,7 @@
 <tables>
-    <table name="bowtie2_indexes" comment_char="#">
+    <table name="bowtie_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-	 	<file path="tool-data/bowtie2_indices.loc" />
+	 	<file path="tool-data/bowtie_indices.loc" />
     </table>
     <table name="tophat_fusion_blastdb_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff -r ae4ed992d98a -r 3279e193b966 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 27 13:11:25 2014 -0500
+++ b/tool_dependencies.xml	Tue Oct 13 12:33:55 2015 -0400
@@ -1,6 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.28">
-        <repository name="package_blast_plus_2_2_28" owner="iuc"/>
+        <repository changeset_revision="5a1b87e367e8" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="tophat2" version="2.0.9">
+        <repository changeset_revision="bac5f59d20d8" name="package_tophat2_2_0_9" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="bowtie" version="0.12.7">
+        <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r ae4ed992d98a -r 3279e193b966 tophat_fusion_post.xml
--- a/tophat_fusion_post.xml	Mon Jan 27 13:11:25 2014 -0500
+++ b/tophat_fusion_post.xml	Tue Oct 13 12:33:55 2015 -0400
@@ -2,14 +2,16 @@
     <description>post-processing to identify fusion genes</description>
     <version_command>tophat-fusion-post --version</version_command>
     <requirements>
-        <requirement type="package">tophat2</requirement>
+        <requirement type="package" version="2.2.28">blast+</requirement>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="2.0.9">tophat2</requirement>
     </requirements>
     <command>
         ## Set up tophat_out structure.
         mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
 
         ## Set up blast directory structure.
-        #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+        #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')
         ln -s ${blast_db_path}/ blast;
 
         ## Set up additional files:
@@ -18,14 +20,14 @@
         ln -s ${blast_db_path}/mcl .;
 
         ## Run tophat-fusion-post
-        tophat-fusion-post -p 22
+        tophat-fusion-post -p \${GALAXY_SLOTS:-4}
         --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
         #if str($is_human) == 'No':
               --non-human
         #end if
 
-	## Bowtie2 indices.
-	${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+	    ## Bowtie indices.
+	    ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')}
     </command>
 
     <inputs>
@@ -47,7 +49,8 @@
     </stdio>
 
     <outputs>
-        <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
+        <data format="tabular" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
         <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
     </outputs>
+    
 </tool>