Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 70:cf4bf94e87d2 draft

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author greg
date Wed, 07 Jun 2017 10:01:51 -0400
parents 61f9552be416
children 7a488497e6c6
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69:61f9552be416 70:cf4bf94e87d2
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 <expand macro="requirements_assembly_post_processor" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 python $__tool_directory__/assembly_post_processor.py
9 python $__tool_directory__/assembly_post_processor.py 9 --transcripts '$input'
10 --transcripts '$input' 10 --prediction_method $prediction_method_cond.prediction_method
11 --prediction_method $prediction_method_cond.prediction_method 11 #if str($prediction_method_cond.prediction_method) == 'estscan':
12 #if str($prediction_method_cond.prediction_method) == 'estscan': 12 --score_matrices '$score_matrices'
13 --score_matrices '$score_matrices' 13 #end if
14 #end if 14 #if str($options_type.options_type_selector) == 'advanced':
15 #if str($options_type.options_type_selector) == 'advanced': 15 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
16 #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':
17 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 17 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
18 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 18 --output_pttgf $output_pttgf
19 --output_pttgf $output_pttgf 19 --output_pttgf_dir $output_pttgf.files_path
20 --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($options_type.strand_specific) == 'yes': 25 --strand_specific 'true'
26 --strand_specific 'true' 26 #end if
27 #end if 27 #if str($options_type.dereplicate) == 'yes':
28 #if str($options_type.dereplicate) == 'yes': 28 --dereplicate 'true'
29 --dereplicate 'true' 29 --output_cleaned_nr_cds '$output_cleaned_nr_cds'
30 --output_cleaned_nr_cds '$output_cleaned_nr_cds' 30 --output_cleaned_nr_pep '$output_cleaned_nr_pep'
31 --output_cleaned_nr_pep '$output_cleaned_nr_pep' 31 #end if
32 #end if 32 --min_length $options_type.min_length
33 --min_length $options_type.min_length 33 #end if
34 #end if 34 --num_threads \${GALAXY_SLOTS:-4}
35 --num_threads \${GALAXY_SLOTS:-4} 35 --output_cds '$output_cds'
36 --output_cds '$output_cds' 36 --output_cleaned_cds '$output_cleaned_cds'
37 --output_cleaned_cds '$output_cleaned_cds' 37 --output_cleaned_pep '$output_cleaned_pep'
38 --output_cleaned_pep '$output_cleaned_pep' 38 --output_pep '$output_pep'
39 --output_pep '$output_pep' 39 ]]></command>
40 ]]>
41 </command>
42 <inputs> 40 <inputs>
43 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 41 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
44 <conditional name="prediction_method_cond"> 42 <conditional name="prediction_method_cond">
45 <param name="prediction_method" type="select" label="Coding regions prediction method"> 43 <param name="prediction_method" type="select" label="Coding regions prediction method">
46 <option value="transdecoder" selected="true">TransDecoder</option> 44 <option value="transdecoder" selected="true">TransDecoder</option>