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1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
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2
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2 <requirements>
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4
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3 <requirement type="package" version="1.2.0">galaxy_protk</requirement>
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4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
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5 </requirements>
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6
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7 <description>Converts a mascot results file to pepXML</description>
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8
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9 <command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
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2
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10 <inputs>
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11
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12 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
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13 <param name="database" type="select" format="text" >
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14 <label>Database</label>
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15 <options from_file="pepxml_databases.loc">
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16 <column name="name" index="0" />
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17 <column name="value" index="2" />
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18 </options>
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19 </param>
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20
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21
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22 </inputs>
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23 <outputs>
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24 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
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25 </outputs>
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26
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27 <help>
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28 Convert mascot results from mascotdat to pepXML
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29 </help>
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30
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31 </tool>
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