Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 86:126430ebebf7 draft

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author greg
date Wed, 25 Oct 2017 08:39:31 -0400
parents b5aac0d2c99c
children e8d7d4a1672f
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85:b5aac0d2c99c 86:126430ebebf7
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement> 7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 python '$__tool_directory__/assembly_post_processor.py' 10 #set output_dir = 'assemblyPostProcessing_dir'
11 AssemblyPostProcessor
11 --transcripts '$input' 12 --transcripts '$input'
12 --prediction_method $prediction_method_cond.prediction_method 13 --prediction_method $prediction_method_cond.prediction_method
13 #if str($prediction_method_cond.prediction_method) == 'estscan': 14 #if str($prediction_method_cond.prediction_method) == 'estscan':
14 --score_matrices '$score_matrices' 15 --score_matrices '$score_matrices'
15 #end if 16 #end if
19 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 20 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
20 --scaffold '$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 --min_coverage $target_gene_family_assembly_cond.min_coverage 24 --min_coverage $target_gene_family_assembly_cond.min_coverage
24 --output_targeted_gene_families_stats '$output_targeted_gene_families_stats'
25 #end if 25 #end if
26 #if str($options_type.strand_specific) == 'yes': 26 #if str($options_type.strand_specific) == 'yes':
27 --strand_specific true 27 --strand_specific true
28 #end if 28 #end if
29 #if str($options_type.dereplicate) == 'yes': 29 #if str($options_type.dereplicate) == 'yes':
30 --dereplicate true 30 --dereplicate true
31 --output_cleaned_nr_cds '$output_cleaned_nr_cds'
32 --output_cleaned_nr_pep '$output_cleaned_nr_pep'
33 #end if 31 #end if
34 --min_length $options_type.min_length 32 --min_length $options_type.min_length
35 #end if 33 #end if
36 --num_threads \${GALAXY_SLOTS:-4} 34 --num_threads \${GALAXY_SLOTS:-4}
37 --output_cds '$output_cds' 35 && mv $output_dir/transcripts.cds '$output_cds'
38 --output_cleaned_cds '$output_cleaned_cds' 36 && mv $output_dir/transcripts.pep '$output_pep'
39 --output_cleaned_pep '$output_cleaned_pep' 37 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
40 --output_pep '$output_pep' 38 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
39 #if str($options_type.options_type_selector) == 'advanced':
40 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
41 && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
42 #end if
43 #if str($options_type.dereplicate) == 'yes':
44 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
45 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
46 #end if
47 #end if
41 ]]></command> 48 ]]></command>
42 <inputs> 49 <inputs>
43 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 50 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
44 <conditional name="prediction_method_cond"> 51 <conditional name="prediction_method_cond">
45 <param name="prediction_method" type="select" label="Coding regions prediction method"> 52 <param name="prediction_method" type="select" label="Coding regions prediction method">