diff defuse.xml @ 2:4245c2b047de

Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl

--- a/defuse.xml	Fri Sep 16 12:41:37 2011 -0500
+++ b/defuse.xml	Tue Nov 08 13:56:35 2011 -0600
@@ -1,10 +1,14 @@
-<tool id="defuse" name="DeFuse" version="1.0">
+<tool id="defuse" name="DeFuse" version="1.1">
  <description>identify fusion transcripts</description>
  <requirements>
   <requirement type="binary"></requirement>
  </requirements>
  <command interpreter="perl">
-  scripts/defuse.pl
+  ## Find the defuse.pl in the galaxy tool path
+  #import Cheetah.FileUtils
+  #set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
+  #set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
+  $defuse
   -c `cp $defuse_config $config_txt; echo $defuse_config`
   -d `mkdir -p data_dir; ln -s $left_pairendreads data_dir/reads_1.fastq; ln -s $right_pairendreads data_dir/reads_2.fastq; echo data_dir`
   -o  output_dir -p 8
@@ -86,20 +90,7 @@
 #
 # At a minimum, change all values enclused by []
 #
-# Gene/Transcript id pattern
-gene_id_pattern = #slurp
-#try
-$ref_dict['gene_id_pattern']
-transcript_id_pattern = #slurp
-#except
-ENSG\d+
-#end try
-#try
-$ref_dict['transcript_id_pattern']
-#except
-ENST\d+
-#end try
-                      
+
 # Directory where the defuse code was unpacked
 ## Default location in the tool/defuse directory  
 # source_directory = ${__root_dir__}/tools/defuse
@@ -107,7 +98,15 @@
 #try
 $ref_dict['source_directory']
 #except
-${__root_dir__}/tools/defuse
+#try
+## Try to find the defuse source dir in the galaxy tool path
+#import Cheetah.FileUtils
+#set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
+#set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
+$defuse.replace('/scripts/defuse.pl','')
+#except
+${__root_dir__}/tools/defuse/defuse
+#end try
 #end try
 
 # Directory where you want your dataset