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author mvdbeek
date Thu, 31 Mar 2016 12:30:01 -0400
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9
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1 <tool id="getgo" name="get_gene_categories" version="0.1.0">
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2 <description>retrieve gene categories for model organisms</description>
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3 <macros>
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4 <import>go_macros.xml</import>
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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><![CDATA[
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9 Rscript $__tool_directory__/getgo.r
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10 --package "$package"
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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 ]]>
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15 </command>
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16 <inputs>
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17 <param help="These are bioconductor genome annotation packages." label="Select the genome package" name="package" size="3" type="select">
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18 <options from_data_table="org_names"></options>
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19 </param>
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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">
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21 <options from_data_table="available_identifiers">
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22 <filter type="param_value" ref="package" column="2"/>
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23 </options>
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24 </param>
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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">
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26 <options from_data_table="available_categories">
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27 <filter type="param_value" ref="package" column="2"/>
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28 </options>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" label="gene category mapping" name="output" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="package" value="org.Hs.eg.db"></param>
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37 <param name="gene_id" value="ENSEMBL"></param>
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38 <param name="cats" value="GO2ALLEGS"></param>
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39 <output name="output" file="go_terms.tab" compare="contains"></output>
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40 </test>
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41 </tests>
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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 This tool uses bioconductor species annotation packages [org.Xx.xx.db] to extract gene category information.
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47 To do gene {category/set} enrichment analysis, use the output of this tool with the goseq tool.
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48
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49 </help>
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50 <citations>
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51 <citation type="bibtex">@ARTICLE{AnnotationDbi,
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52 title = {AnnotationDbi: Annotation Database Interface},
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53 author = {Herve Pages and Marc Carlson and Seth Falcon and Nianhua Li},
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54 note = {R package version 1.32.3}
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55 }
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56 </citation>
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57 </citations>
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58 </tool>