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1 <tool id="dgidb_annotator" name="Annotate with DGI" version="0.1">
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2 <description>database info</description>
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3
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4 <command interpreter="python">
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5 dgidb_annotator.py
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6 #if $expert_curated_only:
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7 -e
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8 #end if
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9 #if $print_all:
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10 -a
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11 #end if
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12 -g $gene_name_col
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13 $input > $output
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14 </command>
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15 <inputs>
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16 <param name="input" label="Input" type="data" format="tabular"/>
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17 <param name="expert_curated_only" label="Use Only Expert Curated Results" type="boolean"/>
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18 <param name="print_all" label="Print All Rows, including those without Annotation" type="boolean"/>
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19 <param name="gene_name_col" label="Gene Name Column" type="data_column" data_ref="input"/>
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20 </inputs>
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21
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22 <outputs>
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23 <data name="output" format="tabular"/>
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24 </outputs>
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25
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26 <stdio>
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27 <regex match=".*" source="both" level="log" description="tool progress"/>
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28 </stdio>
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29
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30 <tests>
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31 <test>
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32 <param name="input" value="in1.tabular"/>
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33 <param name="expert_curated_only" value="True"/>
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34 <param name="print_all" value="False"/>
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35 <param name="gene_name_col" value="1"/>
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36 <output name="output" file="out1.tabular"/>
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37 </test>
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38 </tests>
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39
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40 <help>
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41 Annotates a tabular dataset with information from the `Drug-Gene Interations database`__
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42
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43 .. __: http://dgidb.genome.wustl.edu/
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44 </help>
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45 </tool>
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