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1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0">
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2 <requirements><requirement type="package">protk</requirement></requirements>
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3 <description>Calculate Protein Prophet statistics on search results</description>
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4
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5
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6 <!-- Note .. the input file is assumed to be the first argument -->
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7 <command interpreter="ruby">protein_prophet_wrapper.rb $output $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
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8 <inputs>
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9
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10 <param name="input_file" type="data" format="pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>
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11
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12
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13 <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
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14 <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/>
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15 <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/>
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16 <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
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17 <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
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18 <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
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19 <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
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20 <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
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21 <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
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22 <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>
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23
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24 <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
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25 <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
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26
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27 </inputs>
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28 <outputs>
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29 <data format="protxml" name="output" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" from_work_dir="protein_prophet_results.prot.xml"/>
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30 </outputs>
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31
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32
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33 <!--NOPLOT: do not generate plot png file
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34 NOOCCAM: non-conservative maximum protein list
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35 GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)
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36 NORMPROTLEN: Normalize NSP using Protein Length
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37 LOGPROBS: Use the log of the probabilities in the Confidence calculations
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38 CONFEM: Use the EM to compute probability given the confidence
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39 ALLPEPS: Consider all possible peptides in the database in the confidence model
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40 UNMAPPED: Report results for UNMAPPED proteins
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41 INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
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42 DELUDE: do NOT use peptide degeneracy information when assessing proteins
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43
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44 MINPROB: peptideProphet probabilty threshold (default=0.05)
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45 MININDEP: minimum percentage of independent peptides required for a protein (default=0)
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46
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47
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48 -->
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49
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50 <help>
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51 Run Peptide Prophet
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52 </help>
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53
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54 </tool>
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