Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.xml @ 74:9da5dc4b99cc draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 05 Oct 2017 13:54:37 -0400 |
| parents | b472981ad5c5 |
| children | ce5b201b7782 |
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| 73:b472981ad5c5 | 74:9da5dc4b99cc |
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| 1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.2"> | 1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.3.0"> |
| 2 <description>post-processes de novo transcriptome assembly</description> | 2 <description>post-processes de novo transcriptome assembly</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements_assembly_post_processor" /> | 6 <requirements> |
| 7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement> | |
| 8 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 8 python '$__tool_directory__/assembly_post_processor.py' | 10 python '$__tool_directory__/assembly_post_processor.py' |
| 9 --transcripts '$input' | 11 --transcripts '$input' |
| 10 --prediction_method $prediction_method_cond.prediction_method | 12 --prediction_method $prediction_method_cond.prediction_method |
| 11 #if str($prediction_method_cond.prediction_method) == 'estscan': | 13 #if str($prediction_method_cond.prediction_method) == 'estscan': |
| 13 #end if | 15 #end if |
| 14 #if str($options_type.options_type_selector) == 'advanced': | 16 #if str($options_type.options_type_selector) == 'advanced': |
| 15 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond | 17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond |
| 16 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | 18 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': |
| 17 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' | 19 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' |
| 18 --output_pttgf '$output_pttgf' | 20 --move_stats true |
| 19 --output_pttgf_dir '$output_pttgf.files_path' | |
| 20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' | 21 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' |
| 21 --method '$target_gene_family_assembly_cond.method' | 22 --method '$target_gene_family_assembly_cond.method' |
| 22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming | 23 --gap_trimming $target_gene_family_assembly_cond.gap_trimming |
| 23 #end if | 24 #end if |
| 24 #if str($options_type.strand_specific) == 'yes': | 25 #if str($options_type.strand_specific) == 'yes': |
| 87 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/> | 88 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/> |
| 88 </when> | 89 </when> |
| 89 </conditional> | 90 </conditional> |
| 90 </inputs> | 91 </inputs> |
| 91 <outputs> | 92 <outputs> |
| 92 <data name="output_pttgf" format="pttgf" label="Targeted gene families: ${tool.name} on ${on_string}"> | 93 <collection name="output_tgf" type="list" label="Targeted gene families statistics: ${tool.name} on ${on_string}"> |
| 94 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families_statistics" format="tabular" /> | |
| 93 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> | 95 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> |
| 94 </data> | 96 </collection> |
| 97 <collection name="output_tgf" type="list" label="Targeted gene families: ${tool.name} on ${on_string}"> | |
| 98 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families" format="fasta" /> | |
| 99 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> | |
| 100 </collection> | |
| 95 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/> | 101 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/> |
| 96 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/> | 102 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/> |
| 97 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}"> | 103 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}"> |
| 98 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter> | 104 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter> |
| 99 </data> | 105 </data> |