Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.xml @ 111:233f2d346fd1 draft
Uploaded
author | greg |
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date | Wed, 13 Dec 2017 14:08:36 -0500 |
parents | e2b575f2d346 |
children | 2411671fdc91 |
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110:e2b575f2d346 | 111:233f2d346fd1 |
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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'; |