Mercurial > repos > greg > gene_family_integrator

comparison gene_family_integrator.xml @ 4:9fff0561bc8e draft

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author greg
date Thu, 06 Apr 2017 15:09:50 -0400
parents bbc56c8688ff
children 1d178e90fbe6
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3:d06e3ae4eb5a 4:9fff0561bc8e
14 python $__tool_directory__/gene_family_integrator.py 14 python $__tool_directory__/gene_family_integrator.py
15 --scaffold '$scaffold.fields.path' 15 --scaffold '$scaffold.fields.path'
16 --method $method 16 --method $method
17 #if str($input_format) == 'ptortho': 17 #if str($input_format) == 'ptortho':
18 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 18 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
19 --output '$output_ptortho'
20 --output_dir '$output_ptortho.files_path'
19 #else: 21 #else:
20 ## str($input_format) == 'ptorthocs' 22 ## str($input_format) == 'ptorthocs'
21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 23 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
22 #if str($input_format_cond.orthogroup_fna) == 'yes': 24 #if str($input_format_cond.orthogroup_fna) == 'yes':
23 --orthogroup_fna 'true' 25 --orthogroup_fna 'true'
26 --output '$output_ptorthocs'
27 --output_dir '$output_ptorthocs.files_path'
28 #else:
29 --output '$output_ptortho'
30 --output_dir '$output_ptortho.files_path'
24 #end if 31 #end if
25 #end if 32 #end if
26 --output '$output_html'
27 --output_dir '$output_html.files_path'
28 ]]> 33 ]]>
29 </command> 34 </command>
30 <inputs> 35 <inputs>
31 <conditional name="input_format_cond"> 36 <conditional name="input_format_cond">
32 <param name="input_format" type="select" label="Select type of data to sub sample"> 37 <param name="input_format" type="select" label="Select type of data to sub sample">
45 <expand macro="param_orthogroup_fna" /> 50 <expand macro="param_orthogroup_fna" />
46 </when> 51 </when>
47 </conditional> 52 </conditional>
48 </inputs> 53 </inputs>
49 <outputs> 54 <outputs>
50 <data name="output_html" format="html" /> 55 <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}">
56 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
57 </data>
58 <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}">
59 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
60 </data>
51 </outputs> 61 </outputs>
52 <tests> 62 <tests>
53 <test> 63 <test>
54 </test> 64 </test>
55 </tests> 65 </tests>