Mercurial > repos > jjohnson > defuse
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
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 08 Nov 2011 13:56:35 -0600 |
parents | 36306d8086fa |
children | c90022a13c7c |
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--- 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