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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
author iuc
date Fri, 11 Jan 2019 06:18:00 -0500
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1 <tool id="goslimmer" name="GOSlimmer" version="1.0.1">
2 <description>converts a set of annotation from GO to a given GOSlim version</description>
3 <requirements>
4 <requirement type="package" version="1.0">goslimmer</requirement>
5 </requirements>
6 <command detect_errors="exit_code">goslimmer
7 --go '${go}'
8 --slim '${slim}'
9 --annotation '${annotation}'
10 --output '${output}'
11 </command>
12 <inputs>
13 <param name="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
14 <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
15 <param name="annotation" type="data" format="tabular,txt" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/>
16 </inputs>
17 <outputs>
18 <data name="output" format="tabular" label="Slim Annotations"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="go" ftype="obo" value="go.obo"/>
23 <param name="slim" ftype="obo" value="goslim_generic.obo"/>
24 <param name="annotation" ftype="txt" value="annotations.tab"/>
25 <output name="output" ftype="tabular" file="slim_annotations.tab" lines_diff="0"/>
26 </test>
27 </tests>
28 <help>
29 .. class:: infomark
30
31 GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.
32
33 It requires:
34
35 - A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
36 - A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
37 - A tabular annotation file in GAF (http://geneontology.org/page/download-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one.
38
39 -----
40
41 .. class:: infomark
42
43 GOSlimmer can also be applied to other pairs of OWL/OBO ontologies where one is a subset of the other and you want to convert annotations from the larger to the smaller one.
44 </help>
45 <citations>
46 <citation type="bibtex">
47 @misc{githubgoslimmer,
48 author = {Faria, Daniel},
49 year = {2017},
50 title = {GOSlimmer},
51 publisher = {GitHub},
52 journal = {GitHub repository},
53 url = {https://github.com/DanFaria/GOSlimmer},
54 }
55 </citation>
56 </citations>
57 </tool>