Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.xml @ 104:de1b2dbdd490 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 08 Dec 2017 07:47:15 -0500 |
| parents | 6b071ce71267 |
| children | d5e4dbe5a88f |
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| 103:6b071ce71267 | 104:de1b2dbdd490 |
|---|---|
| 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 &>proc.log | 37 &>proc.log |
| 38 && if [[ $? -ne 0 ]]; then | 38 && if [[ $? -ne 0 ]]; then |
| 39 exec &>/dev/tty; | 39 cp proc.log '$output_cds'; |
| 40 cat proc.log; | 40 cp proc.log '$output_pep'; |
| 41 cp proc.log '$output_cleaned_cds'; | |
| 42 cp proc.log '$output_cleaned_pep'; | |
| 43 #if str($options_type.options_type_selector) == 'advanced': | |
| 44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | |
| 45 cp proc.log '$output_targeted_gene_families_stats'; | |
| 46 #end if | |
| 47 #if str($options_type.dereplicate) == 'yes': | |
| 48 cp proc.log '$output_cleaned_nr_cds'; | |
| 49 cp proc.log '$output_cleaned_nr_pep'; | |
| 50 #end if | |
| 51 #end if | |
| 52 else | |
| 53 mv $output_dir/transcripts.cds '$output_cds'; | |
| 54 mv $output_dir/transcripts.pep '$output_pep'; | |
| 55 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'; | |
| 56 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'; | |
| 57 #if str($options_type.options_type_selector) == 'advanced': | |
| 58 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | |
| 59 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'; | |
| 60 #end if | |
| 61 #if str($options_type.dereplicate) == 'yes': | |
| 62 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'; | |
| 63 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'; | |
| 64 #end if | |
| 65 #end if | |
| 41 fi | 66 fi |
| 42 && mv $output_dir/transcripts.cds '$output_cds' | |
| 43 && mv $output_dir/transcripts.pep '$output_pep' | |
| 44 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' | |
| 45 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' | |
| 46 #if str($options_type.options_type_selector) == 'advanced': | |
| 47 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | |
| 48 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' | |
| 49 #end if | |
| 50 #if str($options_type.dereplicate) == 'yes': | |
| 51 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' | |
| 52 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' | |
| 53 #end if | |
| 54 #end if | |
| 55 ]]></command> | 67 ]]></command> |
| 56 <inputs> | 68 <inputs> |
| 57 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> | 69 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> |
| 58 <conditional name="prediction_method_cond"> | 70 <conditional name="prediction_method_cond"> |
| 59 <param name="prediction_method" type="select" label="Coding regions prediction method"> | 71 <param name="prediction_method" type="select" label="Coding regions prediction method"> |