Mercurial > repos > jjohnson > defuse
comparison 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
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 |