Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 111:233f2d346fd1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 13 Dec 2017 14:08:36 -0500
parents e2b575f2d346
children 2411671fdc91
comparison
equal deleted inserted replaced
110:e2b575f2d346 111:233f2d346fd1
32 --dereplicate 32 --dereplicate
33 #end if 33 #end if
34 --min_length $options_type.min_length 34 --min_length $options_type.min_length
35 #end if 35 #end if
36 --num_threads \${GALAXY_SLOTS:-4} 36 --num_threads \${GALAXY_SLOTS:-4}
37 &>proc.log; 37 &>assembly_post_processor_log.txt;
38 if [[ $? -ne 0 ]]; then 38 if [[ $? -ne 0 ]]; then
39 cp proc.log '$output_cds'; 39 cp assembly_post_processor_log.txt '$output_cds';
40 cp proc.log '$output_pep'; 40 cp assembly_post_processor_log.txt '$output_pep';
41 cp proc.log '$output_cleaned_cds'; 41 cp assembly_post_processor_log.txt '$output_cleaned_cds';
42 cp proc.log '$output_cleaned_pep'; 42 cp assembly_post_processor_log.txt '$output_cleaned_pep';
43 #if str($options_type.options_type_selector) == 'advanced': 43 #if str($options_type.options_type_selector) == 'advanced':
44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
45 cp proc.log '$output_targeted_gene_families_stats'; 45 cp assembly_post_processor_log.txt '$output_targeted_gene_families_stats';
46 #end if 46 #end if
47 #if str($options_type.dereplicate) == 'yes': 47 #if str($options_type.dereplicate) == 'yes':
48 cp proc.log '$output_cleaned_nr_cds'; 48 cp assembly_post_processor_log.txt '$output_cleaned_nr_cds';
49 cp proc.log '$output_cleaned_nr_pep'; 49 cp assembly_post_processor_log.txt '$output_cleaned_nr_pep';
50 #end if 50 #end if
51 #end if 51 #end if
52 exit 1; 52 exit 1;
53 else 53 else
54 mv $output_dir/transcripts.cds '$output_cds'; 54 mv $output_dir/transcripts.cds '$output_cds';