Mercurial > repos > jjohnson > encyclopedia_walnut

annotate encyclopedia_walnut.xml @ 0:925fffecea81 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author jjohnson
date Fri, 19 Jun 2020 10:21:10 -0400
parents
children 114b44e35d30
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925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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1 <tool id="encyclopedia_walnut" name="Walnut" version="@VERSION@.0">
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2 <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CMD_IMPORTS@
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9 @LINK_SCAN_INPUT@
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10 @LINK_FASTA_INPUT@
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11 @LINK_TARGET_FASTA@
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12 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -walnut
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13 @SCAN_INPUT@
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14 @FASTA_INPUT@
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15 @TARGET_FASTA@
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16 @COMMON_OPTIONS@
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17 @MASS_LIBRARY_TOLERANCE@
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18 @PERCOLATOR_OPTIONS@
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19 @PEAK_OPTIONS@
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20 @WINDOW_OPTIONS@
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21 @MODIFICATION_OPTIONS@
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22 @SEARCH_OPTIONS@
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23 -o gxpedia
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24 ]]></command>
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25 <inputs>
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26 <expand macro="scan_input"/>
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27 <expand macro="fasta_input"/>
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28 <expand macro="target_fasta"/>
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29 <expand macro="common_options"/>
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30 <expand macro="mass_library_tolerance"/>
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31 <expand macro="percolator_options"/>
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32 <expand macro="peak_options"/>
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33 <expand macro="window_options"/>
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34 <expand macro="modification_options"/>
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35 <expand macro="search_options"/>
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36 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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37 <option value="log" selected="true">log</option>
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38 <option value="elib" selected="true">elib</option>
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39 <option value="features" selected="true">features.txt</option>
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40 <option value="pecan" selected="true">pecan.txt</option>
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41 <option value="pecan_decoy" selected="true">pecan.decoy.txt</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
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46 <filter>'log' in select_outputs</filter>
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47 </data>
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48 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
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49 <filter>'elib' in select_outputs</filter>
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50 </data>
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51 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
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52 <filter>'features' in select_outputs</filter>
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53 <actions>
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54 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
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55 </actions>
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56 </data>
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57 <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt">
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58 <filter>'pecan' in select_outputs</filter>
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59 <actions>
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60 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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61 </actions>
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62 </data>
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63 <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt">
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64 <filter>'pecan_decoy' in select_outputs</filter>
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65 <actions>
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66 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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67 </actions>
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68 </data>
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69 </outputs>
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70 <help><![CDATA[
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71 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
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72 Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.
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73
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74 Required Parameters:
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75 -i input .DIA or .MZML file
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76 -f background FASTA file
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77
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78 Other Parameters:
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79 -t target FASTA file (default: background FASTA file)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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80 -tp true/false target FASTA file contains peptides (default: false)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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81 -o output report file (default: [input file].pecan.txt)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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82 -acquisition (default: overlapping dia)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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83 -addDecoysToBackground (default: false)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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84 -alpha (default: 1.8)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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85 -beta (default: 0.4)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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86 -dontRunDecoys (default: false)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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87 -enzyme (default: trypsin)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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88 -filterPeaklists (default: false)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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89 -fixed (default: C=57.0214635)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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90 -foffset (default: 0)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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91 -frag (default: YONLY)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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92 -ftol (default: 10)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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93 -ftolunits (default: ppm)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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94 -maxCharge (default: 3)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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95 -maxLength (default: 100)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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96 -maxMissedCleavage (default: 1)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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97 -minCharge (default: 2)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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98 -minEluteTime (default: 12)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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99 -minIntensity (default: -1.0)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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100 -minLength (default: 5)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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101 -minNumOfQuantitativePeaks (default: 3)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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102 -minQuantitativeIonNumber (default: 3)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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103 -numberOfQuantitativePeaks (default: 5)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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104 -numberOfReportedPeaks (default: 1)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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105 -numberOfThreadsUsed (default: 12)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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106 -percolatorProteinThreshold (default: 0.01)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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107 -percolatorThreshold (default: 0.01)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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108 -percolatorVersionNumber (default: 3)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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109 -poffset (default: 0)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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110 -precursorIsolationMargin (default: 0)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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111 -precursorWindowSize (default: -1)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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112 -ptol (default: 10)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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113 -ptolunits (default: ppm)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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114 -requireVariableMods (default: false)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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115 -variable (default: -)
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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116
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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117 ]]></help>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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118 <expand macro="citations" />
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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119 </tool>