Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 96:11e85af74c7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 26 Oct 2017 12:20:04 -0400
parents 7801f23bc5d9
children 9c4afc33bc87
comparison
equal deleted inserted replaced
95:7801f23bc5d9 96:11e85af74c7e
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 && cp $output_dir/transcripts.cds '$output_cds' 37 &>proc.log
38 && cp $output_dir/transcripts.pep '$output_pep' 38 && mv $output_dir/transcripts.cds '$output_cds'
39 && cp $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 39 && mv $output_dir/transcripts.pep '$output_pep'
40 && cp $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 40 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
41 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
41 #if str($options_type.options_type_selector) == 'advanced': 42 #if str($options_type.options_type_selector) == 'advanced':
42 #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':
43 && cp $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' 44 && if [ -f $output_dir/targeted_gene_family_assemblies.stats ]; then
45 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
46 fi
44 #end if 47 #end if
45 #if str($options_type.dereplicate) == 'yes': 48 #if str($options_type.dereplicate) == 'yes':
46 && cp $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 49 && if [ -f $output_dir/transcripts.cleaned.nr.cds ]; then
47 && cp $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' 50 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
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
48 #end if 55 #end if
49 #end if 56 #end if
50 ]]></command> 57 ]]></command>
51 <inputs> 58 <inputs>
52 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 59 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>