Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 72:b3d4fd21506d draft

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Uploaded
author greg
date Tue, 01 Aug 2017 10:32:35 -0400
parents 7a488497e6c6
children b472981ad5c5
comparison
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71:7a488497e6c6 72:b3d4fd21506d
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 <expand macro="requirements_assembly_post_processor" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python $__tool_directory__/assembly_post_processor.py 8 python '$__tool_directory__/assembly_post_processor.py'
9 --transcripts '$input' 9 --transcripts '$input'
10 --prediction_method $prediction_method_cond.prediction_method 10 --prediction_method $prediction_method_cond.prediction_method
11 #if str($prediction_method_cond.prediction_method) == 'estscan': 11 #if str($prediction_method_cond.prediction_method) == 'estscan':
12 --score_matrices '$score_matrices' 12 --score_matrices '$score_matrices'
13 #end if 13 #end if
14 #if str($options_type.options_type_selector) == 'advanced': 14 #if str($options_type.options_type_selector) == 'advanced':
15 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond 15 #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': 16 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
17 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 17 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
18 --output_pttgf $output_pttgf 18 --output_pttgf '$output_pttgf'
19 --output_pttgf_dir $output_pttgf.files_path 19 --output_pttgf_dir '$output_pttgf.files_path'
20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
21 --method '$target_gene_family_assembly_cond.method' 21 --method '$target_gene_family_assembly_cond.method'
22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
23 #end if 23 #end if
24 #if str($options_type.strand_specific) == 'yes': 24 #if str($options_type.strand_specific) == 'yes':
25 --strand_specific 'true' 25 --strand_specific true
26 #end if 26 #end if
27 #if str($options_type.dereplicate) == 'yes': 27 #if str($options_type.dereplicate) == 'yes':
28 --dereplicate 'true' 28 --dereplicate true
29 --output_cleaned_nr_cds '$output_cleaned_nr_cds' 29 --output_cleaned_nr_cds '$output_cleaned_nr_cds'
30 --output_cleaned_nr_pep '$output_cleaned_nr_pep' 30 --output_cleaned_nr_pep '$output_cleaned_nr_pep'
31 #end if 31 #end if
32 --min_length $options_type.min_length 32 --min_length $options_type.min_length
33 #end if 33 #end if