Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 23:1d3e9e154750 draft

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Uploaded
author greg
date Tue, 10 Jan 2017 10:41:42 -0500
parents 035e8b85cdf7
children 93c2ac892a19
comparison
equal deleted inserted replaced
22:035e8b85cdf7 23:1d3e9e154750
21 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 21 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
22 #set create_corresponding_coding_sequences = True 22 #set create_corresponding_coding_sequences = True
23 #else: 23 #else:
24 #set create_corresponding_coding_sequences = False 24 #set create_corresponding_coding_sequences = False
25 #end if 25 #end if
26 #else: 26
27 #set create_corresponding_coding_sequences = False
28 #end if
29
30 #if str($create_orthogroup) == 'yes':
31 #import os 27 #import os
32 #set create_ortho_sequences = True 28 #set create_ortho_sequences = True
33 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 29 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
34 #set dest_dir = $output.extra_files_path 30 #set dest_dir = $output.extra_files_path
31 mkdir -p $dest_dir &&
35 #else: 32 #else:
36 #set create_ortho_sequences = False 33 #set create_ortho_sequences = False
37 #end if 34 #set create_corresponding_coding_sequences = False
38 mkdir -p $dest_dir && 35 #end if
39 #else: 36 #else:
40 #set create_ortho_sequences = False 37 #set create_ortho_sequences = False
38 #set create_corresponding_coding_sequences = False
41 #end if 39 #end if
42 40
43 GeneFamilyClassifier 41 GeneFamilyClassifier
44 --proteins "$input" 42 --proteins "$input"
45 --scaffold "$scaffold" 43 --scaffold "$scaffold"