Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 98:96e4d7bc2f2a draft

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Uploaded
author greg
date Thu, 26 Oct 2017 14:37:24 -0400
parents 9c4afc33bc87
children 01ef9d05d455
comparison
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97:9c4afc33bc87 98:96e4d7bc2f2a
39 && mv $output_dir/transcripts.pep '$output_pep' 39 && mv $output_dir/transcripts.pep '$output_pep'
40 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 40 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
41 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 41 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
42 #if str($options_type.options_type_selector) == 'advanced': 42 #if str($options_type.options_type_selector) == 'advanced':
43 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 43 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
44 && if [ -f "$output_dir/targeted_gene_family_assemblies.stats" ]; then 44 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
45 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
46 fi
47 #end if 45 #end if
48 #if str($options_type.dereplicate) == 'yes': 46 #if str($options_type.dereplicate) == 'yes':
49 && if [ -f "$output_dir/transcripts.cleaned.nr.cds" ]; then 47 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
50 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 48 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
51 fi
52 && if [ -f "$output_dir/transcripts.cleaned.nr.pep" ]; then
53 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
54 fi
55 #end if 49 #end if
56 #end if 50 #end if
57 ]]></command> 51 ]]></command>
58 <inputs> 52 <inputs>
59 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 53 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>