Mercurial > repos > galaxyp > dia_umpire

annotate dia_umpire_quant.xml @ 3:6caa9011f245 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
author galaxyp
date Mon, 04 Mar 2019 11:49:18 -0500
parents e8f7be6a6e59
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1 <tool id="dia_umpire_quant" name="DIA_Umpire_Quant" version="@VERSION@.0">
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2 <description>DIA quantitation and targeted re-extraction</description>
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3 <macros>
3
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4 <import>dia_umpire_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 #import shutil
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11 ### $shutil.copytree($se_input.extra_files_path.__str__,$work_path.__str__)
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12 ## want to save all outputs in a directory output.extra_files_path to be used by
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13 ## Is file naming going to be a problem? May need to have a name param
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14 cat $quant_params > $dia_umpire_quant && echo "Thread = \$GALAXY_SLOTS" >> $dia_umpire_quant
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15 && cp -rp $se_input.extra_files_path.__str__ $work_path.__str__
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16 && ln -s $protxml_input ${work_path}/$interact_prot_xml
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17 && ln -s $searchdb_input ${work_path}/$searchdb_fa
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18 #for $input in $mzxml_inputs:
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19 && ln -s $input ${work_path}/${input.name}
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20 #end for
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21 #for $input in $pepxml_inputs:
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22 && ln -s $input ${work_path}/${input.name}
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23 #end for
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24 ## Make sure pep.xml and prot.xml start with "interact-"
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25 ## && echo "# $quant_params" >> $dia_umpire_quant
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26 && java -jar \$DIA_UMPIRE_QUANT_JAR $quant_params
0
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27 && cp $work_path/ProtSummary*.xls "$ProtSummary"
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28 && cp $work_path/PeptideSummary*.xls "$PeptideSummary"
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29 && cp $work_path/FragSummary*.xls "$FragSummary"
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30 && cp $work_path/IDNoSummary*.xls "$IDNoSummary"
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31 && cat $work_path/*.log "$logfile"
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32 ]]>
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33 </command>
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34
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35 <configfiles>
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36 <configfile name="user_mods"><![CDATA[
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37 <?xml version="1.0"?>
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38 <MSModSpecSet
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39 xmlns="http://www.ncbi.nlm.nih.gov"
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40 xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
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41 xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"
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42 >
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43 <MSModSpec>
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44 <MSModSpec_mod>
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45 <MSMod value="modificationwithneutrallosses">1</MSMod>
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46 </MSModSpec_mod>
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47 <MSModSpec_type>
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48 <MSModType value="modaa">0</MSModType>
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49 </MSModSpec_type>
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50 <MSModSpec_name>test modification with neutral losses</MSModSpec_name>
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51 <MSModSpec_monomass>123.456789</MSModSpec_monomass>
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52 <MSModSpec_averagemass>0</MSModSpec_averagemass>
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53 <MSModSpec_n15mass>0</MSModSpec_n15mass>
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54 <MSModSpec_residues>
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55 <MSModSpec_residues_E>B</MSModSpec_residues_E>
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56 <MSModSpec_residues_E>O</MSModSpec_residues_E>
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57 </MSModSpec_residues>
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58 <MSModSpec_neutralloss>
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59 <MSMassSet>
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60 <MSMassSet_monomass>456.789123</MSMassSet_monomass>
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61 <MSMassSet_averagemass>0</MSMassSet_averagemass>
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62 <MSMassSet_n15mass>0</MSMassSet_n15mass>
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63 </MSMassSet>
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64 <MSMassSet>
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65 <MSMassSet_monomass>789.123456</MSMassSet_monomass>
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66 <MSMassSet_averagemass>0</MSMassSet_averagemass>
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67 <MSMassSet_n15mass>0</MSMassSet_n15mass>
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68 </MSMassSet>
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69 </MSModSpec_neutralloss>
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70 <MSModSpec_unimod>00</MSModSpec_unimod>
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71 <MSModSpec_psi-ms>testMod</MSModSpec_psi-ms>
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72 </MSModSpec>
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73 <MSModSpecSet
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74 ]]>
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75 </configfile>
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76 <configfile name="quant_params"><![CDATA[
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77 #DIA-Umpire (version @VERSION@)
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78 #Data Independent Acquisition data processing and analysis package (Quantitation and targeted re-extraction module)
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79
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80 #Working folder path: the program will process all mzXML files in the working folder (please make sure the corresponding pepXML files are in the same folder with mzXML file)
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81 #Internal spectral library file, output csv files will be stored in the working folder
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82 Path = ${work_path}/
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83
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84 #Or you can specify all DIA mzXML files you want to analyze here (the working folder is still required for storing output files)
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85 # ==File list begin
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86 # ==File list end
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87
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88 #No of threads
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89 Thread = 6
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90
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91 InternalLibID = #if $InternalLibID then $InternalLibID else 'LibID'#
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92
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93 #InternalLibSearch / TargetedExtraction both will work
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94 InternalLibSearch = $TargetedExtraction
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95 ExternalLibSearch = $external_settings.ExternalLibSearch
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96 #if $external_settings.ExternalLibSearch == 'true':
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97 ExternalLibPath = $external_settings.ExternalLibPath
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98 ExternalLibDecoyTag = $external_settings.ExternalLibDecoyTag
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99 ReSearchProb = $external_settings.ReSearchProb
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100 #end if
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101
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102 #Fasta file path
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103 # Fasta = $searchdb_input
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104 Fasta = ${work_path}/$searchdb_fa
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105
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106 #Combined prot.xml file
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107 Combined_Prot = ${work_path}/$interact_prot_xml
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108
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109 #Decoy tag
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110 DecoyPrefix = $DecoyPrefix
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111
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112 #FDR threshold
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113 #if $fdr_settings.advanced == 'yes':
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114 PeptideFDR = #if $fdr_settings.PeptideFDR then $fdr_settings.PeptideFDR else 0.01#
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115 ProteinFDR = #if $fdr_settings.ProteinFDR then $fdr_settings.ProteinFDR else 0.01#
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116 DataSetLevelPepFDR = false
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117 ProbThreshold = #if $fdr_settings.ProbThreshold then $fdr_settings.ProbThreshold else 0.99#
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118 #else
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119 PeptideFDR = 0.01
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120 ProteinFDR = 0.01
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121 ProbThreshold = 0.99
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122 #end if
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123
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124 #UserMod path
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125 #if $usermod.mod_src == 'history':
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126 UserMod= $usermod.UserMods
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127 ## #else if $usermod.mod_src == 'config':
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128 ## UserMod= $user_mods
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129 #else:
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130 UserMod=
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131 #end if
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132
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133 ####Peptide-centric targeted re-extraction####
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134 #file format for external library: traML
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135 ExternalLibPath =
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136 ExternalLibDecoyTag= DECOY
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137 ReSearchProb=0.5
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138
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139 ####Peptide/Fragment selection for MS2-based quantitation####
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140 #if $quant_settings.advanced == 'yes':
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141 ####Peptide filtering####
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142 #Use either peptide group weight (GW) or peptide weight (PepW) to filter non-unique peptide (computed by ProteinProphet),
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143 #Peptides with weight lower than threshold will be removed
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144 FilterWeight = #if $quant_settings.FilterWeight then $quant_settings.FilterWeight else GW#
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145 MinWeight = #if $quant_settings.MinWeight then $quant_settings.MinWeight else 0.9#
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146 ####Peptide/Fragment selection for MS2-based quantitation####
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147 TopNFrag = #if $quant_settings.TopNFrag then $quant_settings.TopNFrag else 6#
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148 TopNPep = #if $quant_settings.TopNPep then $quant_settings.TopNPep else 6#
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149 Freq = #if $quant_settings.Freq then $quant_settings.Freq else 0.5#
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150 #else:
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151 ####Peptide filtering####
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152 #Use either peptide group weight (GW) or peptide weight (PepW) to filter non-unique peptide (computed by ProteinProphet),
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153 #Peptides with weight lower than threshold will be removed
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154 FilterWeight = GW
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155 MinWeight = 0.9
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156 ####Peptide/Fragment selection for MS2-based quantitation####
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157 TopNFrag = 6
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158 TopNPep = 6
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159 Freq = 0.5
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160 #end if
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161 ]]>
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162 </configfile>
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163 </configfiles>
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164
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165 <inputs>
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166 <param name="work_path" type="hidden" value="dia_output_dir"/>
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167 <param name="interact_prot_xml" type="hidden" value="interact.prot.xml"/>
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168 <param name="searchdb_fa" type="hidden" value="searchdb.fasta"/>
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169 <param name="mzxml_inputs" type="data" format="mzxml" multiple="true" label="Proteomics Spectrum files in mzXML format"/>
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170 <param name="pepxml_inputs" type="data" format="pepxml" multiple="true" label="PepXML"/>
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171 <param name="protxml_input" type="data" format="protxml" label="ProtXML"/>
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172 <param name="searchdb_input" type="data" format="fasta" label="Fasta Search Database"/>
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173 <param name="se_input" type="data" format="dia_umpire.ser" label="DIA-Umpire SE Signal Extraction data"/>
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174 <param name="InternalLibID" type="text" value="" label="InternalLibID " >
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175 <help>
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176 InternalLibID: Identifier for the internal spectral library.
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177 If you are processing the dataset for the first time, it will be used as the name for the new library, if you are reprocessing data (e.g. using different thresholds/FDR levels, etc.) first a library with that name will be looked up and used if found.
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178 Recommended value: you can use the same name for all analysis; however it is beneficial to provide unique meaningful names, to make the library more easily reusable.
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179 </help>
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180 </param>
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181
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182 <param name="TargetedExtraction" type="boolean" truevalue="true" falsevalue="false" checked="true" label="TargetedExtraction" >
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183 <help>
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184 Whether to process targeted re-extraction across samples and replicates.
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185 </help>
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186 </param>
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187
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188 <param name="DecoyPrefix" type="text" value="REVERSED_" label="Decoy Prefix in Protein Search FASTA Database" >
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189 <help>
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190 Typical values: if you are unsure what that prefix was, check protein names in the FASTA file. "rev_" and "DECOY_" are common choices.
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191 </help>
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192 </param>
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193
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194 <conditional name="usermod">
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195 <param name="mod_src" type="select" label="User Modifications">
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196 <help>
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197 </help>
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198 <option value="none">none</option>
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199 <option value="history">From history dataset</option>
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200 <!--
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201 <option value="config">Build </option>
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202 -->
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203 </param>
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204 <when value="none"/>
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205 <when value="history">
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206 <param name="UserMods" type="data" format="xml" label="User Modifications OMSSA XML"/>
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207 </when>
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208 </conditional>
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209
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210 <conditional name="external_settings">
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211 <param name="ExternalLibSearch" type="select" label="Use ExternalLibSearch">
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212 <help>
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213 ExternalLibSearch: Whether to process targeted extraction across samples and replicates to research unidentified peptide ions from specified external spectral library. Peptide ions in external library will be research if it satisfies the two conditions. (1) unidentified from initial database search, and (2) unidentified or identified but the probability was lower than the specified threswhold described below.
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214 </help>
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215 <option value="false">no</option>
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216 <option value="true">yes</option>
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217 </param>
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218 <when value="false"/>
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219 <when value="true">
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220 <param name="ExternalLibPath" type="data" format="dia_umpire.ser" label="DIA-Umpire ExternalLibPath">
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221 <help>
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222 ExternalLibPath (new parameter in v1.4): File path of external spectral library file. Currently only traML and custom binary (.serFS) formats are supported, and a decoy spectrum for each forward peptide ion sequence is required in the library file. (Effective only when ExternalLibSearch is set as true)
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223 </help>
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224 </param>
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225 <param name="ExternalLibDecoyTag" type="text" value="DECOY" label="Decoy tag of decoy spectra" >
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226 <help>
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227 ExternalLibDecoyTag: Decoy tag of decoy spectra. (default: DECOY)
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228 </help>
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229 </param>
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230 <param name="ReSearchProb" type="float" value="0.05" optional="true" min=".00" max="1." label="Probability threshold for re-search">
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231 <help>
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232 ReSearchProb: Probability threshold to determine which peptide ion will be re-searched using external spectral library. (default: 0.5)
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233 </help>
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234 </param>
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235 </when>
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236 </conditional>
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237 <!--
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238 -->
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239
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240 <conditional name="fdr_settings">
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241 <param name="advanced" type="select" label="Advanced FDR Estimation Settings" help="Usually do not need to be changed">
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242 <option value="no">no</option>
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243 <option value="yes">yes</option>
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244 </param>
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245 <when value="no"/>
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246 <when value="yes">
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247 <param name="PeptideFDR" type="float" value=".01" optional="true" min=".01" max=".1" label="PeptideFDR" >
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248 <help>
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249 PeptideFDR: Target peptide level FDR.
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250 DIA-Umpire estimates peptide level FDR by target-decoy approach according to peptide ion's maximum PeptideProphet probability. (default: 0.01)
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251 Recommended value: 0.01 or 0.05 are the standard thresholds used in proteomics studies, corresponding to 1% and 5% FDR.
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252 </help>
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253 </param>
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254 <param name="ProteinFDR" type="float" value=".01" optional="true" min=".01" max=".1" label="ProteinFDR" >
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255 <help>
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256 ProteinFDR: Target protein level FDR.
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257 DIA-Umpire fist removes protein identifications with low protein group probability (&lt;0.5) and estimates protein level FDR of the remaining list by target-decoy approach according to the maximum peptide ion probability. (default: 0.01)
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258 Recommended value: 0.01 or 0.05.
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259 </help>
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260 </param>
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261 <param name="ProbThreshold" type="float" value="0.99" optional="true" min=".00" max="1." label="ProbThreshold" >
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262 <help>
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263 ProbThreshold: (0.0~0.99) Probability threshold for peptide-centric targeted extraction. This probability is calculated by DIA-Umpire based on LDA analysis of true and decoy targeted identifications. (default: 0.99)
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264 Recommended value: 0.99 corresponds to 99% confidence in an ID. Which means FDR should be less than 1% in that case.
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265 </help>
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266 </param>
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267 </when>
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268 </conditional>
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269 <!--
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270 -->
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271 <conditional name="quant_settings">
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272 <param name="advanced" type="select" label="Advanced Quantitation Settings" help="Usually do not need to be changed">
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273 <option value="no">no</option>
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274 <option value="yes">yes</option>
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275 </param>
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276 <when value="no"/>
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277 <when value="yes">
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278 <param name="FilterWeight" type="select" label="FilterWeight to remove shared peptides for protein quantitation">
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279 <option value="GW" selected="true">peptide group weight</option>
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280 <option value="PepW">peptide weight</option>
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281 </param>
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282 <param name="MinWeight" type="float" value=".9" optional="true" min="0.0" max="1.0" label="MinWeight" >
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283 <help>
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284 Minimum weight (peptide group weight or peptide weight chosen from the previous option) threshold of peptides to be considered for protein quantitation. Higher weight (closer to 1) of a peptide for a protein is more likely to be a unique peptide for the protein. (default: 0.9)
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285 Recommended value: 0.9
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286 </help>
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287 </param>
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288 <param name="TopNFrag" type="integer" value="6" optional="true" min="1" max="10" label="TopNFrag">
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289 <help>
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290 Top N fragments in terms of fragment score (Pearson correlation fragment intensity) used for determining peptide ion intensity (default:6).
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291 Recommended value: 3 - 6
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292 </help>
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293 </param>
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294 <param name="TopNPep" type="integer" value="6" optional="true" min="1" max="10" label="TopNPep">
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295 <help>
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296 Top N peptide ions in terms of peptide ion intensity (determined by top fragments) used for determining protein intensity (default:6)
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297 Recommended value: 3~6
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298 </help>
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299 </param>
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300 <param name="Freq" type="float" value=".5" optional="true" min=".1" max="1." label="Freq" >
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301 <help>
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302 Minimum frequency of a peptide ion or fragment across all samples/replicates to
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303 be considered for Top N ranking. (default:0.5) Recommended value: 0.5 or more
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304 </help>
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305 </param>
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306 </when>
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307 </conditional>
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308 </inputs>
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309
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310 <outputs>
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311 <data format="txt" name="logfile" label="${tool.name} log"/>
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312 <data format="dia_umpire.quant" name="dia_umpire_quant" label="${tool.name}}"/>
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313 <data format="tabular" name="IDNoSummary" label="${tool.name}} IDNoSummary.xls"/>
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314 <data format="tabular" name="FragSummary" label="${tool.name}} FragSummary.xls"/>
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315 <data format="tabular" name="PeptideSummary" label="${tool.name}} PeptideSummary.xls"/>
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316 <data format="tabular" name="ProtSummary" label="${tool.name}} ProtSummary.xls"/>
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317 </outputs>
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318 <tests>
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319 <test>
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320 </test>
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321 </tests>
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322 <help>
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323 <![CDATA[
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324 =============================================================
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325 **DIA-Umpire quantitation and targeted re-extraction module**
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326 =============================================================
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327
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328 DIA_Umpire_Quant.jar provides quantitation and targeted re-extraction analysis by taking results from Step A signal extraction and Step B untargeted MS/MS database search.
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329
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330 Manual: http://sourceforge.net/projects/diaumpire/files/Manual/DIA_Umpire_Manual_v1.4_pre.pdf
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331
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332 **Input** (DIA-Umpire quantitation and targeted re-extraction module)
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333 =====================================================================
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334
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335 1. Identification results: a .pep.xml result file for each .mgf file and a prot.xml for the entire dataset.
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336 2. Protein sequence database in FASTA format which was used in Step B (untargeted MS/MS database search).
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337 3. All files, including the binary files (.serFS) and .mgf files generated from the signal extraction module, as well as the mzXML files converted from mgf files.
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338 4. Quantitation parameter file (An example "diaumpire.quant_params" can be downloaded at http://goo.gl/wThAVI)
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339
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340 **Parameters** (for parameter file diaumpire.quant_params)
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341 ==========================================================
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342
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343 **Basic parameters** that the users usually need to modify accordingly.
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344
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345 *TargetedExtraction*: Whether to process targeted re-extraction across samples and replicates. Set it as false if you don't want to reprocess data but wish to export quantitation report based on different fragment/peptide selection options
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346
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347 *Fasta*: Path to a protein sequence database in FASTA format which was used for untargeted MS/MS database search.
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348
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349 *Combined_Prot*: Path to the combined ProteinProphet .prot.xml file.
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350
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351 *DecoyPrefix*: Tag/prefix of decoy protein names that you used for protein database search. Typical values: if you are unsure what that prefix was, check protein names in the FASTA file. "rev\_" and "DECOY\_" are common choices.
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352
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353 *InternalLibID*: Identifier for the internal spectral library. If you are processing the dataset for the first time, it will be used as the name for the new library, if you are reprocessing data (e.g. using different thresholds/FDR levels, etc.) first a library with that name will be looked up and used if found. Recommended value: you can use the same name for all analysis; however it is beneficial to provide unique meaningful names, to make the library more easily reusable.
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354
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355 *ExternalLibSearch*: (new parameter in v1.4): Whether to process targeted extraction across samples and replicates to research unidentified peptide ions from specified external spectral library. Peptide ions in external library will be research if it satisfies the two conditions. (1) unidentified from initial database search, and (2) unidentified or identified but the probability was lower than the specified threswhold described below. (Please note that this feature is still being tested, and contact us if you have any questions)
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356
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357 *ExternalLibPath*: (new parameter in v1.4): File path of external spectral library file. Currently only traML and custom binary (.serFS) formats are supported, and a decoy spectrum for each forward peptide ion sequence is required in the library file. (Effective only when ExternalLibSearch is set as true)
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358
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359 *ExternalLibDecoyTag*: (new parameter in v1.4): Decoy tag of decoy spectra. (default: DECOY)
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360
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361 *ReSearchProb*: (new parameter in v1.4): Probability threshold to determine which peptide ion will be re-searched using external spectral library. (default: 0.5)
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362
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363
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364 **Advanced parameters** that usually do **not** need to be changed
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365
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366 **FDR estimation parameters**:
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367
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368 *PeptideFDR*: Target peptide level FDR.
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369 DIA-Umpire estimates peptide level FDR by target-decoy approach according to peptide ion's maximum PeptideProphet probability. (default: 0.01)
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370 Recommended value: 0.01 or 0.05 are the standard thresholds used in proteomics studies, corresponding to 1% and 5% FDR.
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371
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372 *ProteinFDR*: Target protein level FDR.
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373 DIA-Umpire fist removes protein identifications with low protein group probability (<0.5) and estimates protein level FDR of the remaining list by target- decoy approach according to the maximum peptide ion's probability. (default: 0.01)
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374 Recommended value: 0.01 or 0.05.
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375
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376 *ProbThreshold*: (0.0~0.99) Probability threshold for peptide-centric targeted extraction. This probability is calculated by DIA-Umpire based on LDA analysis of true and decoy targeted identifications. (default: 0.99)
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377 Recommended value: 0.99 corresponds to 99% confidence in an ID. Which means FDR should be less than 1% in that case.
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378
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379 **Quantitation parameters**
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380
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381 *FilterWeight*: (GW or PepW) Choice of using peptide group weight or peptide weight (computed by ProteinProphet) to remove shared peptides for protein quantitation. (default: GW)
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382 MinWeight: (0.0~0.99) Minimum weight (peptide group weight or peptide weight chosen from the previous option) threshold of peptides to be considered for protein quantitation. Higher weight (closer to 1) of a peptide for a protein is more likely to be a unique peptide for the protein. (default: 0.9)
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383 Recommended value: 0.9
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384
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385 *TopNFrag*: Top N fragments in terms of fragment score (Pearson correlation x fragment intensity) used for determining peptide ion intensity (default:6).
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386 Recommended value: 3~6
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387
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388 *TopNPep*: Top N peptide ions in terms of peptide ion intensity (determined by top
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389 fragments) used for determining protein intensity (default:6)
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390 Recommended value: 3~6
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391
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392 *Freq*: Minimum frequency of a peptide ion or fragment across all samples/replicates to
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393 be considered for Top N ranking. (default:0.5) Recommended value: 0.5 or more
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394
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395 **Output** (DIA-Umpire quantitation and targeted re-extraction module):
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396 =======================================================================
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397
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398 Binary files which include identification and quantitation information, and possibly the internal spectral library.
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399
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400 Three summary tables for protein, peptide ion, and fragment level reports (<filename> denotes the name of the raw file in which a peptide was identified)
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401
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402 1. Columns printed in protein summary table (ProtSummary.xls)
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403
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404 1. Protein Key: Protein accession number
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405 2. <filename>_Prob: Protein identification probability
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406 3. <filename>_Peptides: Number of identified peptide ions assigned to a protein
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407 4. <filename>_PSMs: Number of identified pseudo MS/MS spectra assigned to a protein
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408 5. <filename>_MS1_iBAQ: Protein abundance estimated by MS1 peptide intensities (See manuscript for details) (iBAQ: sum of all identified peptide intensities divided by the number of theoretical tryptic peptides)
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409 6. <filename>_TopNpep/TopNfra, Freq>freq: Protein abundance estimated by top scored peptide ions and fragments (See manuscript for details).
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410
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411 2. Columns printed in peptide ion summary table (PeptideSummary.xls)
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412
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413 1. Peptide Key: Peptide ion identifier
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414 2. Sequence: Peptide sequence
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415 3. ModSeq: Peptide sequence with modification information
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416 4. Proteins: Parent proteins
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417 5. mz: Precursor m/z of peptide ion
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418 6. Charge: Charge state of peptide ion
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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419 7. MaxProb: Maximum identification probability of peptide ion across the whole data- set from untargeted MS/MS database search
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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420 8. <filename>_Spec_Centric_Prob: Identification probability of a peptide ion from untargeted MS/MS database search
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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421 9. <filename>_Pep_Centric_Prob: Identification probability of a peptide ion from targeted re-extraction matching
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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422 10. <filename>_PSMs: The number of identified pseudo MS/MS spectra assigned to a peptide ion
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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423 11. <filename>_RT: Retention time of a peptide ion
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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424 12. <filename>_MS1: Peptide abundance estimated by MS1 precursor intensity 2.13. <filename>_TopNfra: Peptide abundance estimated by top N fragment ions
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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425
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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426 3. Columns printed in fragment summary table (FragSummary.xls)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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427
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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428 1. Fragment Key: Fragment ion identifier
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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429 2. Protein: Parent protein accession number
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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430 3. Peptide: Parent peptide ion identifier
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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431 4. Fragment: Fragment ion type
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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432 5. FragMz: m/z of fragment ion
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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433 6. <filename>_RT: Retention time of parent peptide ion
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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434 7. <filename>_Spec_Centric_Prob: Identification probability of peptide ion from untargeted MS/MS database search
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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435 8. <filename>_Pep_Centric_Prob: Identification probability of peptide ion from targeted re-extraction matching
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436 9. <filename>_Intensity: fragment intensity
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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437 10. <filename>_Corr: Elution profile Pearson correlation between fragment ion and precursor peptide ion
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438 11. <filename>_PPM: Mass error of an observed fragment m/z to the theoretical one
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439
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440 ]]>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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441 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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442 <expand macro="citations" />
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443 </tool>