Mercurial > repos > greg > plant_tribes_gene_family_integrator

comparison gene_family_integrator.xml @ 1:274f9159ffab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 01 Aug 2017 14:26:05 -0400
parents fa38de0b1f1a
children a322e5e668a3
comparison
equal deleted inserted replaced
0:fa38de0b1f1a 1:274f9159ffab
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'