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annotate idpqonvert.xml @ 10:2ec9bd69259e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
author galaxyp
date Fri, 12 Jun 2020 17:02:53 -0400
parents aec819a9068b
children
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d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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1 <?xml version="1.0"?>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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2 <tool id="idpqonvert" name="idpQonvert" version="@VERSION@.0">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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3 <description>Prepare identification results for IDPicker</description>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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4 <macros>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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5 <import>macros.xml</import>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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6 <xml name="normalizationOptions">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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7 <option value="off" selected="true">None</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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8 <option value="quantile">Quantile</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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9 <option value="linear">Linear</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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10 </xml>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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11 </macros>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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12 <expand macro="requirements" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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13 <stdio>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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14 <exit_code range="1:" level="fatal" description="Job Failed" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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15 <regex match="^Error:.*$" source="both" level="fatal" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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16 </stdio>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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17 <command>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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18 <![CDATA[
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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19 #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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20 #set $input_name = $input.display_name
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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21 #set $output_name = $input_name.split(".")[0] + ".idpDB"
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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22 ln -s '$input' '${input_name}' &&
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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23 ln -s '$ProteinDatabase' '${db_name}' &&
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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24
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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25 idpQonvert
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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26 -DecoyPrefix '${DecoyPrefix}'
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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27 -WriteQonversionDetails true
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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28 -ProteinDatabase '${db_name}'
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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29 -MaxFDR $MaxFDR
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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30 -EmbedSpectrumScanTimes false
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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31 -EmbedSpectrumSources false
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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32 #set $score_info = []
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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33 #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:specevalue", "comet:xcorr", "comet:deltacn", "comet:expect"]
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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34 #set $name = $engine.replace(":", "_").replace("!","")
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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35 #set $weight = $getVar("scoring." + $name + "." + $name + "_weight.value")
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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36 #set $type = $getVar("scoring." + $name + "." + $name + "_type.value")
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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37 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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38 #continue
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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39 #end for
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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40 #for $i, $s in enumerate($scoring.extra_score)
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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41 #set $name = $s.extra_score_name
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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42 #set $type = $s.extra_score_normalization
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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43 #set $weight = $s.extra_score_weight
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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44 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $name]
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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45 #end for
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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46 #set $score_str = "; ".join($score_info)
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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47 -ScoreInfo '$score_str'
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48 -MaxImportFDR $advanced_options.MaxImportFDR
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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49 -MaxResultRank $advanced_options.MaxResultRank
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50 -RerankMatches $advanced_options.RerankMatches
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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51 -Gamma $advanced_options.Gamma
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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52 -Nu $advanced_options.Nu
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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53 -PolynomialDegree $advanced_options.PolynomialDegree
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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54 -TruePositiveThreshold $advanced_options.TruePositiveThreshold
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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55 -MaxTrainingRank $advanced_options.MaxTrainingRank
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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56 -SVMType $advanced_options.SVMType
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57 -Kernel $advanced_options.Kernel
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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58 -ChargeStateHandling $advanced_options.ChargeStateHandling
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59 -TerminalSpecificityHandling $advanced_options.TerminalSpecificityHandling
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60 -MissedCleavagesHandling $advanced_options.MissedCleavagesHandling
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61 -QonverterMethod $advanced_options.QonverterMethod
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62 -MinPartitionSize $advanced_options.MinPartitionSize
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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63 '${input_name}' &&
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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64 mv '$output_name' output
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65 ]]>
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66 </command>
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67 <inputs>
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68 <param name="input" type="data" format="mzid,raw_pepxml" label="Input mzIdentML/pepXML file(s)" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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69 <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to map peptides against. Only peptides from target proteins will be mapped; decoy peptides will be stored as-is in the idpDB." />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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70 <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" help="The prefix to look for on protein accessions to determine whether it is a target or decoy." />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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71 <param argument="-MaxFDR" type="float" label="Max FDR" min="0.0000001" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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72 <section name="advanced_options" title="Advanced Options">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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73 <param argument="-MaxImportFDR" type="float" label="Max Import FDR" min="0.1" value="0.25" help="PSMs with a greater FDR than this will be completely excluded from the idpDB." />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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74 <param argument="-MaxResultRank" type="integer" label="Max Result Rank" min="1" value="2" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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75 <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" min="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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76 <param argument="-RerankMatches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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77 <param argument="-Gamma" type="float" label="Gamma" value="5" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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parents:
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78 <param argument="-Nu" type="float" label="Nu" value="-0.5" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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79 <param argument="-TruePositiveThreshold" type="float" label="True Positive Threshold" min="0.0000001" value="0.01" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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80 <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" min="1" value="3" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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81 <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" min="10" value="10" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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82 <param argument="-SVMType" label="SVM Type" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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83 <option value="CSVC" selected="true">CSVC</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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84 <option value="NuSVC">Nu SCV</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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85 <option value="OneClass">One Class</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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86 <option value="NuSVR">Nu SVR</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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87 <option value="EpsilonSVR">Epsilon SVR</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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88 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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89 <param argument="-Kernel" label="Kernel" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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90 <option value="Linear" selected="true">Linear</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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91 <option value="Polynomial">Polynomial</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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92 <option value="RBR">Radial Basis Function</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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93 <option value="Sigmoid">Sigmoid</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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94 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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95 <param argument="-ChargeStateHandling" label="Charge State Handling" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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96 <option value="Partition" selected="true">Partition</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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97 <option value="Ignore">Ignore</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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98 <option value="Feature">Feature</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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99 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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100 <param argument="-TerminalSpecificityHandling" label="Terminal Specificity Handling" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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101 <option value="Partition" selected="true">Partition</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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102 <option value="Ignore">Ignore</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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103 <option value="Feature">Feature</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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104 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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105 <param argument="-MissedCleavagesHandling" label="Missed Cleavages Handling" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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106 <option value="Ignore" selected="true">Ignore</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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107 <option value="Feature">Feature</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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108 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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109 <param argument="-MassErrorHandling" label="Mass Error Handling" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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110 <option value="Ignore" selected="true">Ignore</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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111 <option value="Feature">Feature</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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112 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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113 <param argument="-QonverterMethod" label="Qonverter Method" type="select">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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114 <option value="MonteCarlo" selected="true">Monte Carlo (recommended)</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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115 <option value="SingleSVM">SVM (single)</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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116 <option value="PartitionSVM">SVM (parition)</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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117 <option value="StaticWeighted">Static Weighted</option>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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118 </param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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119 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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120 <section name="scoring" title="Custom Score Settings">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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121 <section name="myrimatch_mvh" title="Myrimatch (mvh) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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122 <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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123 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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124 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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125 <section name="xcorr" title="Non-Sequest (xcorr) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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126 <param name="xcorr_weight" label="XCorr Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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127 <param name="xcorr_type" label="XCorr Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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128 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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129 <section name="sequest_xcorr" title="Sequest (xcorr) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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130 <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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131 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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132 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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133 <section name="sequest_deltacn" title="Sequest (deltacn) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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134 <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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135 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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136 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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137 <section name="mascot_score" title="Mascot (score) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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138 <param name="mascot_score_weight" label="Mascot Score Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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139 <param name="mascot_score_type" label="Mascot Score Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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140 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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141 <section name="xtandem_expect" title="X! Tandem (expect) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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142 <param name="xtandem_expect_weight" label="X! Tandem (expectation) Weight" type="float" min="-1" max="1" value="-1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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143 <param name="xtandem_expect_type" label="X! Tandem (expectation) Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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144 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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145 <section name="xtandem_hyperscore" title="X! Tandem (hyperscore) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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146 <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" min="-1" max="1" value="1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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147 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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148 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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149 <section name="ms-gf_specevalue" title="MS-GF+ (specevalue) Score/Weight" expanded="False">
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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150 <param name="ms-gf_specevalue_weight" label="MS-GF+ (specevalue) Weight" type="float" min="-1" max="1" value="-1" />
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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151 <param name="ms-gf_specevalue_type" label="MS-GF+ (specevalue) Normalization" type="select"><expand macro="normalizationOptions" /></param>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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152 </section>
d1f7b2395bc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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153 <section name="comet_xcorr" title="Comet (xcorr) Score/Weight" expanded="False">
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154 <param name="comet_xcorr_weight" label="Comet (xcorr) Weight" type="float" min="-1" max="1" value="1" />
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155 <param name="comet_xcorr_type" label="Comet (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
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156 </section>
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157 <section name="comet_deltacn" title="Comet (deltacn) Score/Weight" expanded="False">
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158 <param name="comet_deltacn_weight" label="Comet (deltacn) Weight" type="float" min="-1" max="1" value="1" />
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159 <param name="comet_deltacn_type" label="Comet (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
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160 </section>
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161 <section name="comet_expect" title="Comet (expect) Score/Weight" expanded="False">
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162 <param name="comet_expect_weight" label="Comet (expect) Weight" type="float" min="-1" max="1" value="-1" />
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163 <param name="comet_expect_type" label="Comet (expect) Normalization" type="select"><expand macro="normalizationOptions" /></param>
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164 </section>
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165 <repeat name="extra_score" title="Extra Search Engine Score/Weight">
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166 <param name="extra_score_name" label="Name" type="text" help="For scores in the PSI-MS controlled vocabulary, this field must match the name for that score; for other scores, the UserParam name or pepXML name will suffice." value="SearchEngineName" />
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167 <param name="extra_score_normalization" label="Normalization Method" type="select"><expand macro="normalizationOptions" /></param>
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168 <param name="extra_score_weight" label="Weight" type="float" help="Negative weights indicate that a lower score is better (e.g. expectation value, p-value)." min="-1" max="1" value="1" />
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169 </repeat>
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170 </section>
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171 </inputs>
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172 <outputs>
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173 <data format="idpdb" name="output" from_work_dir="output" />
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174 </outputs>
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175 <tests>
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176 <test>
6
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177 <param name="input" value="201208-378803-mm.pepXML" />
3
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178 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
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179 <param name="MaxFDR" value="0.05" />
6
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180 <output name="output" file="201208-378803-mm.idpDB" compare="sim_size" delta="500000" />
3
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181 </test>
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182 <test>
6
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183 <param name="input" value="201208-378803-cm.pep.xml" />
3
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184 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
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185 <param name="MaxFDR" value="0.05" />
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186 <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
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187 </test>
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188 <test>
6
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189 <param name="input" value="201208-378803-msgf.mzid" />
3
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190 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
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191 <param name="MaxFDR" value="0.05" />
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192 <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
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193 </test>
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194 </tests>
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195 <help>
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196 <![CDATA[
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197 **What it does**
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198
5
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199 Creates IDPicker 3 idpDB files from pepXML and mzIdentML files.
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200 The input files should be unfiltered and must come from a target/decoy database search.
3
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201 ]]>
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202 </help>
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203 <citations>
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204 <citation type="doi">10.1021/pr900360j</citation>
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205 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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206 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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207 </citations>
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208 </tool>