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1 <tool id="mzml_to_mgf_1" name="MzML to mgf" version="1.0.0">
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2 <requirements>
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3 <requirement type="package">protk</requirement>
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4 </requirements>
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5
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6 <description>Converts an mzML file to mgf suitable for searching by omssa</description>
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7
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8 <command>file_convert.rb $input_file -o $output $maldi</command>
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9
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10 <inputs>
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11
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12 <param name="input_file" type="data" format="mzml" multiple="false" label="Input File" help="Line Spectra in mzML format"/>
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13 <param name="maldi" type="boolean" label="Is the data from a MALDI instrument" truevalue="-l" falsevalue=""/>
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14
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15 </inputs>
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16
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17 <outputs>
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18 <data format="mgf" name="output" metadata_source="input_file" label="${input_file.display_name}.mgf" from_work_dir="converted.mgf"/>
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19 </outputs>
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20
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21 <help>
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22 Convert line spectra to Mascot Generic Format
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23 </help>
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24
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25 </tool>
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