Mercurial > repos > greg > assembly_post_processor
changeset 96:11e85af74c7e draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 26 Oct 2017 12:20:04 -0400 |
| parents | 7801f23bc5d9 |
| children | 9c4afc33bc87 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 14 insertions(+), 7 deletions(-) [+] |
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--- a/assembly_post_processor.xml Thu Oct 26 11:41:10 2017 -0400 +++ b/assembly_post_processor.xml Thu Oct 26 12:20:04 2017 -0400 @@ -34,17 +34,24 @@ --min_length $options_type.min_length #end if --num_threads \${GALAXY_SLOTS:-4} -&& cp $output_dir/transcripts.cds '$output_cds' -&& cp $output_dir/transcripts.pep '$output_pep' -&& cp $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' -&& cp $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' +&>proc.log +&& mv $output_dir/transcripts.cds '$output_cds' +&& mv $output_dir/transcripts.pep '$output_pep' +&& mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' +&& mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' #if str($options_type.options_type_selector) == 'advanced': #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': - && cp $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' + && if [ -f $output_dir/targeted_gene_family_assemblies.stats ]; then + mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' + fi #end if #if str($options_type.dereplicate) == 'yes': - && cp $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' - && cp $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' + && if [ -f $output_dir/transcripts.cleaned.nr.cds ]; then + mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' + fi + && if [ -f $output_dir/transcripts.cleaned.nr.pep ]; then + mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' + fi #end if #end if ]]></command>