Mercurial > repos > greg > plant_tribes_assembly_post_processor
comparison assembly_post_processor.xml @ 2:4b6192e96e30 draft
Uploaded
author | greg |
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date | Tue, 01 Aug 2017 14:24:40 -0400 |
parents | cc94680dbc43 |
children | 07ee186ba16e |
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1:cc94680dbc43 | 2:4b6192e96e30 |
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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 |