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annotate goslimmer.xml @ 0:294de027cb5d draft

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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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294de027cb5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
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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 <requirements>
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4 <requirement type="package" version="1.0">goslimmer</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">goslimmer
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7 --go '${go}'
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8 --slim '${slim}'
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9 --annotation '${annotation}'
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10 --output '${output}'
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11 </command>
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12 <inputs>
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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)"/>
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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)"/>
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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)"/>
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="tabular" label="Slim Annotations"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="go" ftype="obo" value="go.obo"/>
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23 <param name="slim" ftype="obo" value="goslim_generic.obo"/>
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24 <param name="annotation" ftype="txt" value="annotations.tab"/>
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25 <output name="output" ftype="tabular" file="slim_annotations.tab" lines_diff="0"/>
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26 </test>
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27 </tests>
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28 <help>
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29 .. class:: infomark
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30
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31 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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32
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33 It requires:
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34
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35 - A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
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36 - A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
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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.
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38
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39 -----
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40
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41 .. class:: infomark
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42
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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.
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44 </help>
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45 <citations>
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46 <citation type="bibtex">
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47 @misc{githubgoslimmer,
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48 author = {Faria, Daniel},
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49 year = {2017},
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50 title = {GOSlimmer},
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51 publisher = {GitHub},
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52 journal = {GitHub repository},
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53 url = {https://github.com/DanFaria/GOSlimmer},
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54 }
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55 </citation>
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56 </citations>
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57 </tool>