Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison gene_family_aligner.xml @ 8:32587f12102c draft

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author greg
date Fri, 22 Jun 2018 08:40:34 -0400
parents 2ac7090847f9
children 1c5a484fc06f
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7:2ac7090847f9 8:32587f12102c
13 #for $i in $input: 13 #for $i in $input:
14 #set filename = $i.file_name 14 #set filename = $i.file_name
15 #set name = $i.name 15 #set name = $i.name
16 ln -s $filename $input_dir/$name && 16 ln -s $filename $input_dir/$name &&
17 #end for 17 #end for
18 export TOOLS_DIR=\$(dirname `which GeneFamilyAligner`) &&
19 export PASTA_TOOLS_RUNDIR=\$TOOLS_DIR &&
20 export PASTA_TOOLS_DEVDIR=\$TOOLS_DIR &&
18 GeneFamilyAligner 21 GeneFamilyAligner
19 --alignment_method $alignment_method 22 --alignment_method $alignment_method
20 #if str($alignment_method) == 'pasta': 23 #if str($alignment_method) == 'pasta':
21 --pasta_script_path '$__tool_directory__/run_pasta.py' 24 --pasta_script_path '$__tool_directory__/run_pasta.py'
22 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 25 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit