Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison getgo.xml @ 9:04b9c519d3e1 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 6574ffcb63770ff8de2d496894292cb7ce0492a8
author mvdbeek
date Thu, 31 Mar 2016 12:23:45 -0400
parents 0e9424413ab0
children
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8:fb95db039592 9:04b9c519d3e1
1 <tool id="getgo" name="getgo" version="0.1.0"> 1 <tool id="getgo" name="get_gene_categories" version="0.1.0">
2 <description>downloads gene ontologies for model organisms</description> 2 <description>retrieve gene categories for model organisms</description>
3 <macros> 3 <macros>
4 <import>go_macros.xml</import> 4 <import>go_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command interpreter="Rscript"> 8 <command><![CDATA[
9 getgo.r --genome "$genome" 9 Rscript $__tool_directory__/getgo.r
10 --gtf "$gtf" 10 --package "$package"
11 --gene_id "$gene_id" 11 --gene_id "$gene_id"
12 --output "$output" 12 --output "$output"
13 --cats "$cats" 13 --cats "$cats"
14 ]]>
14 </command> 15 </command>
15 <inputs> 16 <inputs>
16 <param name="gtf" label="select GTF file" help="GO annotations for all gene ids in this GTF will be fetched" type="data" format="gtf"/> 17 <param help="These are bioconductor genome annotation packages." label="Select the genome package" name="package" size="3" type="select">
17 <param help="Needed to retrieve GO annotations for the selected genome" label="Select the genome source" name="genome" size="3" type="select"> 18 <options from_data_table="org_names"></options>
18 <options from_data_table="go_genomes"></options>
19 </param> 19 </param>
20 <param help="Needed for GO analysis" label="Select gene identifier format" name="gene_id" type="select"> 20 <param help="This option determines which gene identifier format is used for mapping genes to categories in the output file. If you have a list of differentially expressed genes, choose the same format." label="Select gene identifier format" name="gene_id" type="select">
21 <options from_data_table="go_gene_ids"></options> 21 <options from_data_table="available_identifiers">
22 <filter type="param_value" ref="package" column="2"/>
23 </options>
22 </param> 24 </param>
23 <param name="cats" help="Select the categories for which you would like to retrieve ontologies" type="select" multiple="true" display="checkboxes"> 25 <param name="cats" label="Select categories" help="Select a category will return the category and a list of all genes in that category" type="select" multiple="true" display="checkboxes">
24 <option value="GO:CC">GO:Cellular Components</option> 26 <options from_data_table="available_categories">
25 <option value="GO:BP">BiologicalProcesses</option> 27 <filter type="param_value" ref="package" column="2"/>
26 <option value="GO:MF">Molecular Function</option> 28 </options>
27 <option value="KEGG">KEGG pathway</option>
28 </param> 29 </param>
29 </inputs> 30 </inputs>
30 <outputs> 31 <outputs>
31 <data format="tabular" label="GO category mapping" name="output" /> 32 <data format="tabular" label="gene category mapping" name="output" />
32 </outputs> 33 </outputs>
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <param name="gtf" value="in.gtf" ftype="gtf"></param> 36 <param name="package" value="org.Hs.eg.db"></param>
36 <param name="genome" value="hg38"></param> 37 <param name="gene_id" value="ENSEMBL"></param>
37 <param name="gene_id" value="ensGene"></param> 38 <param name="cats" value="GO2ALLEGS"></param>
38 <param name="cats" value="GO:CC,GO:BP,GO:MF"></param> 39 <output name="output" file="go_terms.tab" compare="contains"></output>
39 <output name="output" file="go_terms.tab"></output>
40 </test> 40 </test>
41 </tests> 41 </tests>
42 <help> 42 <help>
43 43
44 **What it does** 44 **What it does**
45 45
46 Returns a tabular file with GO gene categories for all genes present in the input GTF file. 46 This tool uses bioconductor species annotation packages [org.Xx.xx.db] to extract gene category information.
47 47 To do gene {category/set} enrichment analysis, use the output of this tool with the goseq tool.
48 48
49 </help> 49 </help>
50 <citations> 50 <citations>
51 <citation type="doi">10.1186/gb-2010-11-2-r14</citation> 51 <citation type="bibtex">@ARTICLE{AnnotationDbi,
52 title = {AnnotationDbi: Annotation Database Interface},
53 author = {Herve Pages and Marc Carlson and Seth Falcon and Nianhua Li},
54 note = {R package version 1.32.3}
55 }
56 </citation>
52 </citations> 57 </citations>
53 </tool> 58 </tool>