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comparison assembly_post_processor.xml @ 95:7801f23bc5d9 draft

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Uploaded
author greg
date Thu, 26 Oct 2017 11:41:10 -0400
parents 33915a72ae4e
children 11e85af74c7e
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94:33915a72ae4e 95:7801f23bc5d9
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 && mv $output_dir/transcripts.cds '$output_cds' 37 && cp $output_dir/transcripts.cds '$output_cds'
38 && mv $output_dir/transcripts.pep '$output_pep' 38 && cp $output_dir/transcripts.pep '$output_pep'
39 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 39 && cp $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
40 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 40 && cp $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
41 #if str($options_type.options_type_selector) == 'advanced': 41 #if str($options_type.options_type_selector) == 'advanced':
42 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 42 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
43 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' 43 && cp $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
44 #end if 44 #end if
45 #if str($options_type.dereplicate) == 'yes': 45 #if str($options_type.dereplicate) == 'yes':
46 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 46 && cp $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
47 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' 47 && cp $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
48 #end if 48 #end if
49 #end if 49 #end if
50 ]]></command> 50 ]]></command>
51 <inputs> 51 <inputs>
52 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 52 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>