Mercurial > repos > greg > plant_tribes_assembly_post_processor
changeset 5:2732db7dd0ef draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 21 Dec 2017 09:13:41 -0500 |
| parents | b0d9dc3c8535 |
| children | c197d5306cd6 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 30 insertions(+), 14 deletions(-) [+] |
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--- a/assembly_post_processor.xml Mon Oct 30 09:51:13 2017 -0400 +++ b/assembly_post_processor.xml Thu Dec 21 09:13:41 2017 -0500 @@ -34,21 +34,37 @@ --min_length $options_type.min_length #end if --num_threads \${GALAXY_SLOTS:-4} -&>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': - && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' +&>assembly_post_processor_log.txt; +if [[ $? -ne 0 ]]; then + cp assembly_post_processor_log.txt '$output_cds'; + cp assembly_post_processor_log.txt '$output_pep'; + cp assembly_post_processor_log.txt '$output_cleaned_cds'; + cp assembly_post_processor_log.txt '$output_cleaned_pep'; + #if str($options_type.options_type_selector) == 'advanced': + #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': + cp assembly_post_processor_log.txt '$output_targeted_gene_families_stats'; + #end if + #if str($options_type.dereplicate) == 'yes': + cp assembly_post_processor_log.txt '$output_cleaned_nr_cds'; + cp assembly_post_processor_log.txt '$output_cleaned_nr_pep'; + #end if #end if - #if str($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' + exit 1; +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 -#end if - ]]></command> +fi]]></command> <inputs> <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> <conditional name="prediction_method_cond"> @@ -168,7 +184,7 @@ assembled transcripts into putative coding sequences and their corresponding amino acid translations and optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the -de novo assembly. +de novo assembly. -----