Mercurial > repos > greg > plant_tribes_assembly_post_processor
comparison assembly_post_processor.xml @ 5:2732db7dd0ef draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 21 Dec 2017 09:13:41 -0500 |
| parents | b0d9dc3c8535 |
| children | c197d5306cd6 |
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| 4:b0d9dc3c8535 | 5:2732db7dd0ef |
|---|---|
| 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 &>proc.log | 37 &>assembly_post_processor_log.txt; |
| 38 && mv $output_dir/transcripts.cds '$output_cds' | 38 if [[ $? -ne 0 ]]; then |
| 39 && mv $output_dir/transcripts.pep '$output_pep' | 39 cp assembly_post_processor_log.txt '$output_cds'; |
| 40 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' | 40 cp assembly_post_processor_log.txt '$output_pep'; |
| 41 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' | 41 cp assembly_post_processor_log.txt '$output_cleaned_cds'; |
| 42 #if str($options_type.options_type_selector) == 'advanced': | 42 cp assembly_post_processor_log.txt '$output_cleaned_pep'; |
| 43 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | 43 #if str($options_type.options_type_selector) == 'advanced': |
| 44 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats' | 44 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': |
| 45 #end if | 45 cp assembly_post_processor_log.txt '$output_targeted_gene_families_stats'; |
| 46 #if str($options_type.dereplicate) == 'yes': | 46 #end if |
| 47 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' | 47 #if str($options_type.dereplicate) == 'yes': |
| 48 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' | 48 cp assembly_post_processor_log.txt '$output_cleaned_nr_cds'; |
| 49 #end if | 49 cp assembly_post_processor_log.txt '$output_cleaned_nr_pep'; |
| 50 #end if | 50 #end if |
| 51 ]]></command> | 51 #end if |
| 52 exit 1; | |
| 53 else | |
| 54 mv $output_dir/transcripts.cds '$output_cds'; | |
| 55 mv $output_dir/transcripts.pep '$output_pep'; | |
| 56 mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'; | |
| 57 mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'; | |
| 58 #if str($options_type.options_type_selector) == 'advanced': | |
| 59 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | |
| 60 mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'; | |
| 61 #end if | |
| 62 #if str($options_type.dereplicate) == 'yes': | |
| 63 mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'; | |
| 64 mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'; | |
| 65 #end if | |
| 66 #end if | |
| 67 fi]]></command> | |
| 52 <inputs> | 68 <inputs> |
| 53 <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"/> |
| 54 <conditional name="prediction_method_cond"> | 70 <conditional name="prediction_method_cond"> |
| 55 <param name="prediction_method" type="select" label="Coding regions prediction method"> | 71 <param name="prediction_method" type="select" label="Coding regions prediction method"> |
| 56 <option value="transdecoder" selected="true">TransDecoder</option> | 72 <option value="transdecoder" selected="true">TransDecoder</option> |
| 166 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and | 182 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and |
| 167 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo | 183 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo |
| 168 assembled transcripts into putative coding sequences and their corresponding amino acid translations and | 184 assembled transcripts into putative coding sequences and their corresponding amino acid translations and |
| 169 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been | 185 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been |
| 170 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the | 186 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the |
| 171 de novo assembly. | 187 de novo assembly. |
| 172 | 188 |
| 173 ----- | 189 ----- |
| 174 | 190 |
| 175 **Required options** | 191 **Required options** |
| 176 | 192 |