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comparison gene_family_integrator.xml @ 29:2fc444a858b6 draft

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author greg
date Wed, 25 Oct 2017 11:30:26 -0400
parents a22dd6959e5a
children 435b622bae05
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28:a22dd6959e5a 29:2fc444a858b6
16 #end for 16 #end for
17 GeneFamilyIntegrator 17 GeneFamilyIntegrator
18 --orthogroup_fasta '$input_dir' 18 --orthogroup_fasta '$input_dir'
19 --scaffold '$scaffold.fields.path' 19 --scaffold '$scaffold.fields.path'
20 --method $method 20 --method $method
21 &>proc.log
21 ]]></command> 22 ]]></command>
22 <inputs> 23 <inputs>
23 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Classified orthogroup fasta files" /> 24 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Classified orthogroup fasta files" />
24 <expand macro="param_scaffold" /> 25 <expand macro="param_scaffold" />
25 <expand macro="param_method" /> 26 <expand macro="param_method" />
28 <collection name="output" type="list" label="${tool.name} (integrated gene family clusters) on ${on_string}"> 29 <collection name="output" type="list" label="${tool.name} (integrated gene family clusters) on ${on_string}">
29 <discover_datasets pattern="__name__" directory="integratedGeneFamilies_dir" format="fasta" /> 30 <discover_datasets pattern="__name__" directory="integratedGeneFamilies_dir" format="fasta" />
30 </collection> 31 </collection>
31 </outputs> 32 </outputs>
32 <tests> 33 <tests>
33 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
34 <test> 34 <test>
35 <param name="input">
36 <collection type="list">
37 <element name="3722.faa" value="3722.faa"/>
38 <element name="3722.fna" value="3722.fna"/>
39 <element name="38889.faa" value="38889.faa"/>
40 <element name="38889.fna" value="38889.fna"/>
41 <element name="39614.faa" value="39614.faa"/>
42 <element name="39614.fna" value="39614.fna"/>
43 </collection>
44 </param>
45 <param name="scaffold" value="22Gv1.1"/>
46 <param name="method" value="orthomcl"/>
47 <output_collection name="output" type="list">
48 <element name="3722.faa" file="3722_integrated.faa" ftype="fasta"/>
49 <element name="3722.fna" file="3722_integrated.fna" ftype="fasta"/>
50 <element name="38889.faa" file="38889_integrated.faa" ftype="fasta"/>
51 <element name="38889.fna" file="38889_integrated.fna" ftype="fasta"/>
52 <element name="39614.faa" file="39614_integrated.faa" ftype="fasta"/>
53 <element name="39614.fna" file="39614_integrated.fna" ftype="fasta"/>
54 </output_collection>
35 </test> 55 </test>
36 -->
37 </tests> 56 </tests>
38 <help> 57 <help>
39 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 58 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
40 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone 59 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone
41 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool. 60 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool.