Mercurial > repos > greg > gene_family_integrator

comparison gene_family_integrator.xml @ 24:3e4215484c68 draft

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author greg
date Tue, 01 Aug 2017 10:37:38 -0400
parents 80996fca62c8
children 47db4f99b31f
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23:80996fca62c8 24:3e4215484c68
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format 8 #set input_format = $input_format_cond.input_format
9 #set scaffold = $input_format_cond.scaffold 9 #set scaffold = $input_format_cond.scaffold
10 #set method = $input_format_cond.method 10 #set method = $input_format_cond.method
11 11
12 python $__tool_directory__/gene_family_integrator.py 12 python '$__tool_directory__/gene_family_integrator.py'
13 --scaffold '$scaffold.fields.path' 13 --scaffold '$scaffold.fields.path'
14 --method $method 14 --method $method
15 #if str($input_format) == 'ptortho': 15 #if str($input_format) == 'ptortho':
16 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 16 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
17 --output '$output_ptortho' 17 --output '$output_ptortho'
18 --output_dir '$output_ptortho.files_path' 18 --output_dir '$output_ptortho.files_path'
19 #else: 19 #else:
20 ## str($input_format) == 'ptorthocs' 20 ## str($input_format) == 'ptorthocs'
21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
22 #if str($input_format_cond.orthogroup_fna) == 'yes': 22 #if str($input_format_cond.orthogroup_fna) == 'yes':
23 --orthogroup_fna 'true' 23 --orthogroup_fna true
24 --output '$output_ptorthocs' 24 --output '$output_ptorthocs'
25 --output_dir '$output_ptorthocs.files_path' 25 --output_dir '$output_ptorthocs.files_path'
26 #else: 26 #else:
27 --output '$output_ptortho' 27 --output '$output_ptortho'
28 --output_dir '$output_ptortho.files_path' 28 --output_dir '$output_ptortho.files_path'