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comparison gene_family_integrator.xml @ 26:b91bf5a51d38 draft

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author greg
date Wed, 04 Oct 2017 11:08:10 -0400
parents 47db4f99b31f
children 346dc0d9af6f
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25:47db4f99b31f 26:b91bf5a51d38
1 <tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.2"> 1 <tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.3.0">
2 <description>integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences</description> 2 <description>integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_integrator" /> 6 <expand macro="requirements_gene_family_integrator" />
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_dir = 'input_dir'
9 #set scaffold = $input_format_cond.scaffold 9 mkdir $input_dir &&
10 #set method = $input_format_cond.method 10 #for $i in $input:
11 11 #set filename = $i.file_name
12 python '$__tool_directory__/gene_family_integrator.py' 12 #set name = $i.name
13 ln -s $filename $input_dir/$name &&
14 #end for
15 GeneFamilyIntegrator
16 --orthogroup_fasta '$input_dir'
13 --scaffold '$scaffold.fields.path' 17 --scaffold '$scaffold.fields.path'
14 --method $method 18 --method $method
15 #if str($input_format) == 'ptortho':
16 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
17 --output '$output_ptortho'
18 --output_dir '$output_ptortho.files_path'
19 #else:
20 ## str($input_format) == 'ptorthocs'
21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
22 #if str($input_format_cond.orthogroup_fna) == 'yes':
23 --orthogroup_fna true
24 --output '$output_ptorthocs'
25 --output_dir '$output_ptorthocs.files_path'
26 #else:
27 --output '$output_ptortho'
28 --output_dir '$output_ptortho.files_path'
29 #end if
30 #end if
31 ]]></command> 19 ]]></command>
32 <inputs> 20 <inputs>
33 <conditional name="input_format_cond"> 21 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" />
34 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 22 <expand macro="param_scaffold" />
35 <option value="ptortho">Proteins orthogroup fasta files</option> 23 <expand macro="param_method" />
36 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
37 </param>
38 <when value="ptortho">
39 <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
40 <validator type="empty_extra_files_path" />
41 </param>
42 <expand macro="param_scaffold" />
43 <expand macro="param_method" />
44 </when>
45 <when value="ptorthocs">
46 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
47 <validator type="empty_extra_files_path" />
48 </param>
49 <expand macro="param_scaffold" />
50 <expand macro="param_method" />
51 <expand macro="param_orthogroup_fna" />
52 </when>
53 </conditional>
54 </inputs> 24 </inputs>
55 <outputs> 25 <outputs>
56 <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}"> 26 <collection name="output" type="list" label="${tool.name} (integrated gene family clusters) on ${on_string}">
57 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> 27 <discover_datasets pattern="__name__" directory="integratedGeneFamilies_dir" format="fasta" />
58 </data> 28 </collection>
59 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}">
60 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
61 </data>
62 </outputs> 29 </outputs>
63 <tests> 30 <tests>
64 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 31 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
65 <test> 32 <test>
66 </test> 33 </test>