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1 <tool id="trams" name="TRAMS">
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2 <description>Tool for Rapid Annotation of Microbial SNPs</description>
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3 <command interpreter="python">trams.py $input1 $input2 $ref_format $annot $overl $sum</command>
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4 <inputs>
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5 <param name="input1" type="data" format="tabular" label="SNP table" />
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6 <param name="input2" type="data" format="txt" label="Reference genome" help="Reference genome file, should be genbank or embl file." />
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7 <param name="ref_format" type="select">
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8 <label>Reference file type</label>
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9 <option value="gb">Genbank</option>
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10 <option value="embl">EMBL</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data name="annot" format="tabular" label="${tool.name} on ${on_string}: SNP annotation file" />
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15 <data name="overl" format="tabular" label="${tool.name} on ${on_string}: Overlap file" />
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16 <data name="sum" format="txt" label="${tool.name} on ${on_string}: Summary file" />
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17 </outputs>
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18 <help>
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19
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20 This tool annotates SNPs from a SNP table and a genbank file.
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21
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22 </help>
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23 </tool>
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