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comparison defuse.xml @ 2:4245c2b047de

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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 13:56:35 -0600
parents 36306d8086fa
children c90022a13c7c
comparison
equal deleted inserted replaced
1:36306d8086fa 2:4245c2b047de
1 <tool id="defuse" name="DeFuse" version="1.0"> 1 <tool id="defuse" name="DeFuse" version="1.1">
2 <description>identify fusion transcripts</description> 2 <description>identify fusion transcripts</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary"></requirement> 4 <requirement type="binary"></requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="perl"> 6 <command interpreter="perl">
7 scripts/defuse.pl 7 ## Find the defuse.pl in the galaxy tool path
8 #import Cheetah.FileUtils
9 #set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
10 #set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
11 $defuse
8 -c `cp $defuse_config $config_txt; echo $defuse_config` 12 -c `cp $defuse_config $config_txt; echo $defuse_config`
9 -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` 13 -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`
10 -o output_dir -p 8 14 -o output_dir -p 8
11 </command> 15 </command>
12 <inputs> 16 <inputs>
84 # 88 #
85 # Configuration file for defuse 89 # Configuration file for defuse
86 # 90 #
87 # At a minimum, change all values enclused by [] 91 # At a minimum, change all values enclused by []
88 # 92 #
89 # Gene/Transcript id pattern 93
90 gene_id_pattern = #slurp
91 #try
92 $ref_dict['gene_id_pattern']
93 transcript_id_pattern = #slurp
94 #except
95 ENSG\d+
96 #end try
97 #try
98 $ref_dict['transcript_id_pattern']
99 #except
100 ENST\d+
101 #end try
102
103 # Directory where the defuse code was unpacked 94 # Directory where the defuse code was unpacked
104 ## Default location in the tool/defuse directory 95 ## Default location in the tool/defuse directory
105 # source_directory = ${__root_dir__}/tools/defuse 96 # source_directory = ${__root_dir__}/tools/defuse
106 source_directory = #slurp 97 source_directory = #slurp
107 #try 98 #try
108 $ref_dict['source_directory'] 99 $ref_dict['source_directory']
109 #except 100 #except
110 ${__root_dir__}/tools/defuse 101 #try
102 ## Try to find the defuse source dir in the galaxy tool path
103 #import Cheetah.FileUtils
104 #set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
105 #set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
106 $defuse.replace('/scripts/defuse.pl','')
107 #except
108 ${__root_dir__}/tools/defuse/defuse
109 #end try
111 #end try 110 #end try
112 111
113 # Directory where you want your dataset 112 # Directory where you want your dataset
114 dataset_directory = #slurp 113 dataset_directory = #slurp
115 #try 114 #try