Mercurial > repos > devteam > dgidb_annotator
comparison dgidb_annotator.xml @ 0:8c6dc9da6c89 draft
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| author | devteam |
|---|---|
| date | Wed, 27 Nov 2013 23:51:48 -0500 |
| parents | |
| children | c5bb987015c5 |
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| -1:000000000000 | 0:8c6dc9da6c89 |
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| 1 <tool id="dgidb_annotator" name="Annotate with DGI" version="0.1"> | |
| 2 <description>database info</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 dgidb_annotator.py | |
| 6 #if $expert_curated_only: | |
| 7 -e | |
| 8 #end if | |
| 9 #if $print_all: | |
| 10 -a | |
| 11 #end if | |
| 12 -g $gene_name_col | |
| 13 $input > $output | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="input" label="Input" type="data" format="tabular"/> | |
| 17 <param name="expert_curated_only" label="Use Only Expert Curated Results" type="boolean"/> | |
| 18 <param name="print_all" label="Print All Rows, including those without Annotation" type="boolean"/> | |
| 19 <param name="gene_name_col" label="Gene Name Column" type="data_column" data_ref="input"/> | |
| 20 </inputs> | |
| 21 | |
| 22 <outputs> | |
| 23 <data name="output" format="tabular"/> | |
| 24 </outputs> | |
| 25 | |
| 26 <stdio> | |
| 27 <regex match=".*" source="both" level="log" description="tool progress"/> | |
| 28 </stdio> | |
| 29 | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input" value="in1.tabular"/> | |
| 33 <param name="expert_curated_only" value="True"/> | |
| 34 <param name="print_all" value="False"/> | |
| 35 <param name="gene_name_col" value="1"/> | |
| 36 <output name="output" file="out1.tabular"/> | |
| 37 </test> | |
| 38 </tests> | |
| 39 | |
| 40 <help> | |
| 41 Annotates a tabular dataset with information from the `Drug-Gene Interations database`__ | |
| 42 | |
| 43 .. __: http://dgidb.genome.wustl.edu/ | |
| 44 </help> | |
| 45 </tool> |