Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 107:67420bf2013b draft

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Uploaded
author greg
date Fri, 08 Dec 2017 09:01:01 -0500
parents d0cb6804592c
children 0bc8487c0e2e
comparison
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106:d0cb6804592c 107:67420bf2013b
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 &>proc.log
38 && if [[ $? -ne 0 ]]; 38 && if [[ $? -ne 0 ]]; then
39 then 39 cp proc.log '$output_cds';
40 cp proc.log '$output_cds' 40 cp proc.log '$output_pep';
41 cp proc.log '$output_pep' 41 cp proc.log '$output_cleaned_cds';
42 cp proc.log '$output_cleaned_cds' 42 cp proc.log '$output_cleaned_pep';
43 cp proc.log '$output_cleaned_pep'
44 #if str($options_type.options_type_selector) == 'advanced': 43 #if str($options_type.options_type_selector) == 'advanced':
45 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
46 cp proc.log '$output_targeted_gene_families_stats' 45 cp proc.log '$output_targeted_gene_families_stats';
47 #end if 46 #end if
48 #if str($options_type.dereplicate) == 'yes': 47 #if str($options_type.dereplicate) == 'yes':
49 cp proc.log '$output_cleaned_nr_cds' 48 cp proc.log '$output_cleaned_nr_cds';
50 cp proc.log '$output_cleaned_nr_pep' 49 cp proc.log '$output_cleaned_nr_pep';
51 #end if 50 #end if
52 #end if 51 #end if
53 else 52 else
54 mv $output_dir/transcripts.cds '$output_cds' 53 mv $output_dir/transcripts.cds '$output_cds';
55 mv $output_dir/transcripts.pep '$output_pep' 54 mv $output_dir/transcripts.pep '$output_pep';
56 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 55 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds';
57 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 56 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep';
58 #if str($options_type.options_type_selector) == 'advanced': 57 #if str($options_type.options_type_selector) == 'advanced':
59 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 58 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
60 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' 59 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats';
61 #end if 60 #end if
62 #if str($options_type.dereplicate) == 'yes': 61 #if str($options_type.dereplicate) == 'yes':
63 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 62 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds';
64 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' 63 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep';
65 #end if 64 #end if
66 #end if 65 #end if
67 fi]]></command> 66 fi]]></command>
68 <inputs> 67 <inputs>
69 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 68 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>