Mercurial > repos > greg > plant_tribes_assembly_post_processor
comparison assembly_post_processor.xml @ 5:2732db7dd0ef draft
Uploaded
author | greg |
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date | Thu, 21 Dec 2017 09:13:41 -0500 |
parents | b0d9dc3c8535 |
children | c197d5306cd6 |
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4:b0d9dc3c8535 | 5:2732db7dd0ef |
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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 |