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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit 2983eca17b9a004685024b6f4554a5190d63c7fd
author iuc
date Wed, 24 Jul 2019 05:37:26 -0400
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1 <tool id="goslimmer" name="GOSlimmer" version="1.0.1">
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2 <description>converts a set of annotation from GO to a given GOSlim version</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.0">goslimmer</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">goslimmer
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10 --go '${go}'
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11 --slim '${slim}'
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12 --annotation '${annotation}'
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13 --output '${output}'
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14 </command>
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15 <inputs>
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16 <param name="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
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17 <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
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18 <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)"/>
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19 </inputs>
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20 <outputs>
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21 <data name="output" format="tabular" label="Slim Annotations"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="go" ftype="obo" value="go.obo"/>
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26 <param name="slim" ftype="obo" value="goslim_generic.obo"/>
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27 <param name="annotation" ftype="txt" value="annotations.tab"/>
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28 <output name="output" ftype="tabular" file="slim_annotations.tab" lines_diff="0"/>
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29 </test>
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30 </tests>
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31 <help>
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32 .. class:: infomark
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34 GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.
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35
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36 It requires:
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37
1
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38 - A full Gene Ontology file in either OBO or OWL format (see @ONTOLOGY_URL@).
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39 - A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
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40 - A tabular annotation file in GAF (@ANNOTATION_URL@) 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.
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42 -----
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44 .. class:: infomark
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45
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46 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.
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47 </help>
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48 <citations>
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49 <citation type="bibtex">
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50 @misc{githubgoslimmer,
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51 author = {Faria, Daniel},
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52 year = {2017},
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53 title = {GOSlimmer},
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54 publisher = {GitHub},
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55 journal = {GitHub repository},
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56 url = {https://github.com/DanFaria/GOSlimmer},
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57 }
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58 </citation>
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59 </citations>
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60 </tool>