Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 21:795745116516 draft

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Uploaded
author greg
date Tue, 10 Jan 2017 10:33:47 -0500
parents 038777896b71
children 035e8b85cdf7
comparison
equal deleted inserted replaced
20:038777896b71 21:795745116516
10 <regex match="Error:" /> 10 <regex match="Error:" />
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': 15 #if str($options_type.options_type_selector) == 'advanced':
16 #import os
17 #set create_ortho_sequences = True
18 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
19 #set dest_dir = $output.extra_files_path
20 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 16 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
21 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 17 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
22 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 18 #if str($create_orthogroup) == 'yes':
23 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 19 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
24 #set create_corresponding_coding_sequences = True 20 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
21 #set create_corresponding_coding_sequences = True
22 #else:
23 #set create_corresponding_coding_sequences = False
25 #else: 24 #else:
26 #set create_corresponding_coding_sequences = False 25 #set create_corresponding_coding_sequences = False
26 #end if
27 #if str($create_orthogroup) == 'yes':
28 #import os
29 #set create_ortho_sequences = True
30 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
31 #set dest_dir = $output.extra_files_path
32 #else:
33 #set create_ortho_sequences = False
27 #end if 34 #end if
28 mkdir -p $dest_dir && 35 mkdir -p $dest_dir &&
29 #else: 36 #else:
30 #set create_ortho_sequences = False 37 #set create_ortho_sequences = False
31 #end if 38 #end if