Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 106:d0cb6804592c draft

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Uploaded
author greg
date Fri, 08 Dec 2017 08:52:26 -0500
parents d5e4dbe5a88f
children 67420bf2013b
comparison
equal deleted inserted replaced
105:d5e4dbe5a88f 106:d0cb6804592c
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 ]]; then 38 && if [[ $? -ne 0 ]];
39 cp proc.log '$output_cds'; 39 then
40 cp proc.log '$output_pep'; 40 cp proc.log '$output_cds'
41 cp proc.log '$output_cleaned_cds'; 41 cp proc.log '$output_pep'
42 cp proc.log '$output_cleaned_pep'; 42 cp proc.log '$output_cleaned_cds'
43 cp proc.log '$output_cleaned_pep'
43 #if str($options_type.options_type_selector) == 'advanced': 44 #if str($options_type.options_type_selector) == 'advanced':
44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 45 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
45 cp proc.log '$output_targeted_gene_families_stats'; 46 cp proc.log '$output_targeted_gene_families_stats'
46 #end if 47 #end if
47 #if str($options_type.dereplicate) == 'yes': 48 #if str($options_type.dereplicate) == 'yes':
48 cp proc.log '$output_cleaned_nr_cds'; 49 cp proc.log '$output_cleaned_nr_cds'
49 cp proc.log '$output_cleaned_nr_pep'; 50 cp proc.log '$output_cleaned_nr_pep'
50 #end if 51 #end if
51 #end if 52 #end if
52 else 53 else
53 mv $output_dir/transcripts.cds '$output_cds'; 54 mv $output_dir/transcripts.cds '$output_cds'
54 mv $output_dir/transcripts.pep '$output_pep'; 55 mv $output_dir/transcripts.pep '$output_pep'
55 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'; 56 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
56 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'; 57 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
57 #if str($options_type.options_type_selector) == 'advanced': 58 #if str($options_type.options_type_selector) == 'advanced':
58 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 59 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
59 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'; 60 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
60 #end if 61 #end if
61 #if str($options_type.dereplicate) == 'yes': 62 #if str($options_type.dereplicate) == 'yes':
62 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'; 63 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
63 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'; 64 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
64 #end if 65 #end if
65 #end if 66 #end if
66 fi]]></command> 67 fi]]></command>
67 <inputs> 68 <inputs>
68 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 69 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>