Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate getgo.xml @ 6:0e9424413ab0 draft

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author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents b79c65c90744
children 04b9c519d3e1
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6
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mvdbeek
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1 <tool id="getgo" name="getgo" version="0.1.0">
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2 <description>downloads gene ontologies for model organisms</description>
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3 <macros>
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mvdbeek
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4 <import>go_macros.xml</import>
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mvdbeek
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command interpreter="Rscript">
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9 getgo.r --genome "$genome"
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10 --gtf "$gtf"
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11 --gene_id "$gene_id"
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12 --output "$output"
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13 --cats "$cats"
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14 </command>
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15 <inputs>
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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"/>
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17 <param help="Needed to retrieve GO annotations for the selected genome" label="Select the genome source" name="genome" size="3" type="select">
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18 <options from_data_table="go_genomes"></options>
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19 </param>
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20 <param help="Needed for GO analysis" label="Select gene identifier format" name="gene_id" type="select">
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21 <options from_data_table="go_gene_ids"></options>
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22 </param>
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23 <param name="cats" help="Select the categories for which you would like to retrieve ontologies" type="select" multiple="true" display="checkboxes">
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24 <option value="GO:CC">GO:Cellular Components</option>
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25 <option value="GO:BP">BiologicalProcesses</option>
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26 <option value="GO:MF">Molecular Function</option>
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27 <option value="KEGG">KEGG pathway</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" label="GO category mapping" name="output" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="gtf" value="in.gtf" ftype="gtf"></param>
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36 <param name="genome" value="hg38"></param>
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37 <param name="gene_id" value="ensGene"></param>
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38 <param name="cats" value="GO:CC,GO:BP,GO:MF"></param>
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39 <output name="output" file="go_terms.tab"></output>
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40 </test>
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41 </tests>
5
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42 <help>
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43
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44 **What it does**
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45
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46 Returns a tabular file with GO gene categories for all genes present in the input GTF file.
5
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47
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48
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49 </help>
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50 <citations>
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51 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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52 </citations>
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53 </tool>