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comparison gene_family_integrator.xml @ 23:80996fca62c8 draft

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author greg
date Thu, 08 Jun 2017 10:01:41 -0400
parents b08f999574db
children 3e4215484c68
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22:1a54a0ba5a81 23:80996fca62c8
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"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 #set input_format = $input_format_cond.input_format
9 #set input_format = $input_format_cond.input_format 9 #set scaffold = $input_format_cond.scaffold
10 #set scaffold = $input_format_cond.scaffold 10 #set method = $input_format_cond.method
11 #set method = $input_format_cond.method
12 11
13 python $__tool_directory__/gene_family_integrator.py 12 python $__tool_directory__/gene_family_integrator.py
14 --scaffold '$scaffold.fields.path' 13 --scaffold '$scaffold.fields.path'
15 --method $method 14 --method $method
16 #if str($input_format) == 'ptortho': 15 #if str($input_format) == 'ptortho':
17 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 16 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
18 --output '$output_ptortho' 17 --output '$output_ptortho'
19 --output_dir '$output_ptortho.files_path' 18 --output_dir '$output_ptortho.files_path'
20 #else: 19 #else:
21 ## str($input_format) == 'ptorthocs' 20 ## str($input_format) == 'ptorthocs'
22 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
23 #if str($input_format_cond.orthogroup_fna) == 'yes': 22 #if str($input_format_cond.orthogroup_fna) == 'yes':
24 --orthogroup_fna 'true' 23 --orthogroup_fna 'true'
25 --output '$output_ptorthocs' 24 --output '$output_ptorthocs'
26 --output_dir '$output_ptorthocs.files_path' 25 --output_dir '$output_ptorthocs.files_path'
27 #else: 26 #else:
28 --output '$output_ptortho' 27 --output '$output_ptortho'
29 --output_dir '$output_ptortho.files_path' 28 --output_dir '$output_ptortho.files_path'
30 #end if 29 #end if
31 #end if 30 #end if
32 ]]> 31 ]]></command>
33 </command>
34 <inputs> 32 <inputs>
35 <conditional name="input_format_cond"> 33 <conditional name="input_format_cond">
36 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 34 <param name="input_format" type="select" label="Classified orthogroup fasta files">
37 <option value="ptortho">Proteins orthogroup fasta files</option> 35 <option value="ptortho">Proteins orthogroup fasta files</option>
38 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option> 36 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
61 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}"> 59 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}">
62 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter> 60 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
63 </data> 61 </data>
64 </outputs> 62 </outputs>
65 <tests> 63 <tests>
64 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
66 <test> 65 <test>
67 <param name="input_format" value="ptorthocs"/>
68 <param name="input_ptorthocs" value="input.ptorthocs" ftype="ptorthocs"/>
69 <param name="scaffold" value="22Gv1.1"/>
70 <param name="method" value="orthomcl"/>
71 <param name="classifier" value="both"/>
72 <param name="orthogroup_fna" value="yes"/>
73 <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
74 </test> 66 </test>
67 -->
75 </tests> 68 </tests>
76 <help> 69 <help>
77 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 70 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
78 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone 71 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone
79 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool. 72 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool.