comparison gene_family_integrator.xml @ 3:276f0f31ddb0 draft

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author greg
date Mon, 30 Oct 2017 09:53:09 -0400
parents a322e5e668a3
children 8ef8997aaa0c
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2:a322e5e668a3 3:276f0f31ddb0
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 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_integrator</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format 10 #set input_dir = 'input_dir'
9 #set scaffold = $input_format_cond.scaffold 11 mkdir $input_dir &&
10 #set method = $input_format_cond.method 12 #for $i in $input:
11 13 #set filename = $i.file_name
12 python '$__tool_directory__/gene_family_integrator.py' 14 #set name = $i.name
15 ln -s $filename $input_dir/$name &&
16 #end for
17 GeneFamilyIntegrator
18 --orthogroup_fasta '$input_dir'
13 --scaffold '$scaffold.fields.path' 19 --scaffold '$scaffold.fields.path'
14 --method $method 20 --method $method
15 #if str($input_format) == 'ptortho': 21 &>proc.log
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> 22 ]]></command>
32 <inputs> 23 <inputs>
33 <conditional name="input_format_cond"> 24 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Classified orthogroup fasta files" />
34 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 25 <expand macro="param_scaffold" />
35 <option value="ptortho">Proteins orthogroup fasta files</option> 26 <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> 27 </inputs>
55 <outputs> 28 <outputs>
56 <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}"> 29 <collection name="output" type="list" label="${tool.name} (integrated gene family clusters) on ${on_string}">
57 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> 30 <discover_datasets pattern="__name__" directory="integratedGeneFamilies_dir" format="fasta" />
58 </data> 31 </collection>
59 <data name="output_ptorthocs" format="ptorthocs" label="${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> 32 </outputs>
63 <tests> 33 <tests>
64 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
65 <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>
66 </test> 55 </test>
67 -->
68 </tests> 56 </tests>
69 <help> 57 <help>
70 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
71 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
72 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.
77 65
78 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences. 66 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
79 67
80 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Data Manager tool. 68 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
81 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. 69 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
82
83 **Other options**
84
85 * **Orthogroups coding sequences** - Select 'Yes' to create corresponding coding sequences orthogroup fasta files for the classified protein sequences.
86
87 </help> 70 </help>
88 <citations> 71 <citations>
89 <expand macro="citation1" /> 72 <expand macro="citation1" />
90 <citation type="bibtex"> 73 <citation type="bibtex">
91 @article{Wall2008, 74 @article{Wall2008,