Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 74:9da5dc4b99cc draft

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author greg
date Thu, 05 Oct 2017 13:54:37 -0400
parents b472981ad5c5
children ce5b201b7782
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73:b472981ad5c5 74:9da5dc4b99cc
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>