Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 104:de1b2dbdd490 draft

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Uploaded
author greg
date Fri, 08 Dec 2017 07:47:15 -0500
parents 6b071ce71267
children d5e4dbe5a88f
comparison
equal deleted inserted replaced
103:6b071ce71267 104:de1b2dbdd490
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 [[ $? -ne 0 ]]; then
39 exec &>/dev/tty; 39 cp proc.log '$output_cds';
40 cat proc.log; 40 cp proc.log '$output_pep';
41 cp proc.log '$output_cleaned_cds';
42 cp proc.log '$output_cleaned_pep';
43 #if str($options_type.options_type_selector) == 'advanced':
44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
45 cp proc.log '$output_targeted_gene_families_stats';
46 #end if
47 #if str($options_type.dereplicate) == 'yes':
48 cp proc.log '$output_cleaned_nr_cds';
49 cp proc.log '$output_cleaned_nr_pep';
50 #end if
51 #end if
52 else
53 mv $output_dir/transcripts.cds '$output_cds';
54 mv $output_dir/transcripts.pep '$output_pep';
55 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds';
56 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep';
57 #if str($options_type.options_type_selector) == 'advanced':
58 #if str($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 #end if
61 #if str($options_type.dereplicate) == 'yes':
62 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds';
63 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep';
64 #end if
65 #end if
41 fi 66 fi
42 && mv $output_dir/transcripts.cds '$output_cds'
43 && mv $output_dir/transcripts.pep '$output_pep'
44 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
45 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
46 #if str($options_type.options_type_selector) == 'advanced':
47 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
48 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
49 #end if
50 #if str($options_type.dereplicate) == 'yes':
51 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
52 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
53 #end if
54 #end if
55 ]]></command> 67 ]]></command>
56 <inputs> 68 <inputs>
57 <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"/>
58 <conditional name="prediction_method_cond"> 70 <conditional name="prediction_method_cond">
59 <param name="prediction_method" type="select" label="Coding regions prediction method"> 71 <param name="prediction_method" type="select" label="Coding regions prediction method">