Mercurial > repos > greg > assembly_post_processor
changeset 104:de1b2dbdd490 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 08 Dec 2017 07:47:15 -0500 |
| parents | 6b071ce71267 |
| children | d5e4dbe5a88f |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 27 insertions(+), 15 deletions(-) [+] |
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--- a/assembly_post_processor.xml Thu Dec 07 15:25:30 2017 -0500 +++ b/assembly_post_processor.xml Fri Dec 08 07:47:15 2017 -0500 @@ -36,22 +36,34 @@ --num_threads \${GALAXY_SLOTS:-4} &>proc.log && if [[ $? -ne 0 ]]; then - exec &>/dev/tty; - cat proc.log; + cp proc.log '$output_cds'; + cp proc.log '$output_pep'; + cp proc.log '$output_cleaned_cds'; + cp proc.log '$output_cleaned_pep'; + #if str($options_type.options_type_selector) == 'advanced': + #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': + cp proc.log '$output_targeted_gene_families_stats'; + #end if + #if str($options_type.dereplicate) == 'yes': + cp proc.log '$output_cleaned_nr_cds'; + cp proc.log '$output_cleaned_nr_pep'; + #end if + #end if +else + 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': + mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'; + #end if + #if str($options_type.dereplicate) == 'yes': + mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'; + mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'; + #end if + #end if fi -&& 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': - && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' - #end if - #if str($options_type.dereplicate) == 'yes': - && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' - && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' - #end if -#end if ]]></command> <inputs> <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>