annotate msgfplus.xml @ 6:4b7d768b74d3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 11837caf01413f2657b529b7cd7a4ec0960110fa
author galaxyp
date Fri, 27 Oct 2017 13:04:49 -0400
parents ce4882b95b73
children f8873f2afc6f
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1 <tool id="msgfplus" name="MS-GF+" version="0.3.1">
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2 <description>
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3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
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4 </description>
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5 <requirements>
2
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6 <requirement type="package" version="2016.10.26">msgf_plus</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Job Failed" />
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10 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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11 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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12 </stdio>
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13 <command>
2
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14
0
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15 <![CDATA[
2
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16 #if $msgf_input.intype_selector == "single"
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17 #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta"
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18 #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML"
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19 ln -s '$msgf_input.s' '${input_name}' &&
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20 ln -s '$msgf_input.d' '${db_name}' &&
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21 #else if $msgf_input.intype_selector == "fractions"
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22 #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta"
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23 #set $input_name = $msgf_input.db_spectra.name.replace(".mzML", "") + ".mzML"
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24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' &&
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25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' &&
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26 #end if
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27 #set $output_name = $input_name.replace(".mzML", ".mzid")
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28
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29 echo \\#Mods > Mods.txt &&
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30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
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31 #for $mod in $common_mods.split(",")
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32 echo '$mod.replace("_", ",")' >> Mods.txt &&
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33 #end for
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34
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35 #for $mod in $custom_mods
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36 #set aa_nocomma = str($mod.aa_specificity).replace(",", "")
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37 echo '${mod.formula_or_mass},${aa_nocomma},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
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38 #end for
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39
6
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40 msgf_plus
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41 -s '$input_name'
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42 -d '$db_name'
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43 -thread \${GALAXY_SLOTS:-1}
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44 -mod Mods.txt
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45 -tda $tda
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46 -t $t$precursor_ion_tol_units
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47 -ti $advanced.isotope_low,$advanced.isotope_high
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48 -m $advanced.m
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49 -inst $inst
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50 -e $e
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51 -protocol $advanced.protocol
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52 -ntt $ntt
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53 -minLength $advanced.minLength
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54 -maxLength $advanced.maxLength
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55 -minCharge $advanced.minCharge
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56 -maxCharge $advanced.maxCharge
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57 -n $advanced.n
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58 -addFeatures $advanced.addFeatures
6
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59 #if $tsvcheck
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60 &&
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61 msgf_plus
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62 edu.ucsd.msjava.ui.MzIDToTsv
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63 -i '$output_name'
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64 -o output.tsv
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65 #end if
0
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66 &&
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67 mv '$output_name' output
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68 ]]>
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69 </command>
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70 <inputs>
2
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71 <conditional name="msgf_input">
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72 <param name="intype_selector" type="select" label="Type of MSGF+ analysis">
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73 <option value="single">Single database</option>
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74 <option value="fractions">Prefractionated database</option>
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75 </param>
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76 <when value="single">
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77 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
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78 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
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79 </when>
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80 <when value="fractions">
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81 <param name="db_spectra" type="data_collection" collection_type="paired"
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82 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
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83 </when>
2
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84 </conditional>
3
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85 <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
0
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86 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
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87 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
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88 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
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89 <option value="ppm" selected="true">Parts per million (ppm)</option>
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90 <option value="Da">Daltons</option>
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91 </param>
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92 <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model">
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93 <option value="0" selected="true">Low-res (LCQ/LTQ)</option>
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94 <option value="1" >High-res (LTQ-Orbitrap)</option>
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95 <option value="2" >Q-TOF</option>
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96 <option value="3" >Q-Exactive</option>
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97 </param>
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98 <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme">
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99 <option value="0">Unspecific cleavage</option>
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100 <option value="1" selected="true">Trypsin, no P rule</option>
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101 <option value="2">Chymotrypsin, no P rule (FYWL)</option>
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102 <option value="3">Lys-C, no P rule</option>
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103 <option value="4">Lys-N</option>
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104 <option value="5">Glu-C (glutamyl endopeptidase)</option>
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105 <option value="6">Arg-C</option>
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106 <option value="7">Asp-N</option>
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107 <option value="8">Alpha-lytic protease</option>
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108 <option value="9">No enzyme</option>
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109 </param>
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110 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more.">
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111 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option>
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112 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
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113 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
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114 </param>
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115
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116 <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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117 <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option>
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118 <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option>
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119 <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option>
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120 <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option>
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121 <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option>
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122 <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option>
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123 <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option>
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124 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
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125 </param>
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126 <param name="common_variable_modifications" type="select" label="Common Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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127 <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option>
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128 <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option>
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129 <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option>
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130 <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option>
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131 <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option>
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132 <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option>
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133 <option value="CH2_K_opt_any_Methyl">Methylation K</option>
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134 <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option>
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135 <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option>
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136 <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option>
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137 <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option>
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138 <option value="H-2O-1_E_opt_N-term_Glu-&gt;pyro-Glu">Pyro-glu from E</option>
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139 <option value="H-3N-1_Q_opt_N-term_Gln-&gt;pyro-Glu">Pyro-glu from Q</option>
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140 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
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141 </param>
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142
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143 <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters">
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144 <param name="formula_or_mass" type="text" label="Formula or Mass">
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145 <sanitizer>
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146 <valid initial="string.digits">
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147 <add value="C"/>
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148 <add value="H"/>
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149 <add value="O"/>
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150 <add value="N"/>
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151 <add value="S"/>
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152 <add value="P"/>
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153 <add value="B"/><add value="r"/>
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154 <add value="C"/><add value="l"/>
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155 <add value="F"/><add value="e"/>
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156 <add value="S"/>
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157 <add value="."/>
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158 <add value="-"/>
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159 </valid>
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160 </sanitizer>
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161 </param>
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162 <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity">
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163 <option value="*" selected="true">Any</option>
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164 <option value="A">A</option>
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165 <option value="C">C</option>
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166 <option value="D">D</option>
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167 <option value="E">E</option>
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168 <option value="F">F</option>
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169 <option value="G">G</option>
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170 <option value="H">H</option>
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171 <option value="I">I</option>
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172 <option value="K">K</option>
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173 <option value="L">L</option>
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174 <option value="M">M</option>
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175 <option value="N">N</option>
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176 <option value="P">P</option>
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177 <option value="Q">Q</option>
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178 <option value="R">R</option>
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179 <option value="S">S</option>
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180 <option value="T">T</option>
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181 <option value="V">V</option>
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182 <option value="W">W</option>
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183 <option value="Y">Y</option>
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184 </param>
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185 <param name="fix_or_opt" type="select" label="Variable or Fixed?">
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186 <option value="opt" selected="true">Variable</option>
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187 <option value="fix">Fixed</option>
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188 </param>
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189 <param name="position_specificity" type="select" label="Positional Specificity">
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190 <option value="any" selected="true">Any</option>
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191 <option value="n-term">Peptide N-terminal</option>
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192 <option value="c-term">Peptide C-terminal</option>
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193 <option value="prot-n-term">Protein N-terminal</option>
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194 <option value="prot-c-term">Protein C-terminal</option>
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195 </param>
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196 <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" />
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197 </repeat>
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198
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199 <!-- MS-GF+ ADVANCED PARAMETERS -->
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200 <section name="advanced" title="Advanced Options">
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201 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/>
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202 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/>
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203 <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/>
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204 <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/>
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205 <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" />
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206 <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
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207 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
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208 <option value="1" >CID</option>
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209 <option value="2" >ETD</option>
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210 <option value="3" >HCD</option>
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211 </param>
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212 <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples">
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213 <option value="0" selected="True">Automatic</option>
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214 <option value="1" >Phosphorylation</option>
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215 <option value="2" >iTRAQ</option>
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216 <option value="3" >iTRAQPhospho</option>
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217 <option value="4" >TMT</option>
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218 <option value="5" >Standard</option>
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219 </param>
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220 <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
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221 <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" />
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222 <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" />
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223 <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" />
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224 </section>
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225 </inputs>
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226 <outputs>
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227 <data name="output" format="mzid" from_work_dir="output" />
3
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228 <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" >
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229 <filter>tsvcheck</filter>
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230 </data>
0
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231 </outputs>
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232 <tests>
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233 <test>
3
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234 <param name="msgf_input|intype_selector" value="single" />
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235 <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" />
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236 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" />
2
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237 <param name="tda" value="1" />
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238 <param name="ntt" value="1" />
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239 <param name="t" value="50" />
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240 <param name="precursor_ion_tol_units" value="ppm" />
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241 <param name="common_fixed_modifications" value="" />
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242 <param name="common_variable_modifications" value="" />
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243 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
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244 </test>
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245 <test>
3
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246 <param name="msgf_input|intype_selector" value="single" />
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247 <param name="msgf_input|s" value="input/201208-378803.mzML" />
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248 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
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249 <param name="tsvcheck" value="true" />
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250 <param name="tda" value="1" />
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251 <param name="ntt" value="1" />
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252 <param name="t" value="50" />
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253 <param name="precursor_ion_tol_units" value="ppm" />
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254 <param name="common_fixed_modifications" value="" />
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255 <param name="common_variable_modifications" value="" />
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256 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
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257 <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" />
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258 </test>
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259 <test>
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260 <param name="msgf_input|intype_selector" value="fractions" />
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261 <param name="msgf_input|db_spectra">
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262 <collection type="paired">
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263 <element name="forward" value="input/201208-378803.mzML" />
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264 <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" />
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265 </collection>
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266 </param>
0
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267 <param name="tda" value="1" />
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268 <param name="ntt" value="1" />
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269 <param name="t" value="50" />
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270 <param name="precursor_ion_tol_units" value="ppm" />
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271 <param name="common_fixed_modifications" value="" />
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272 <param name="common_variable_modifications" value="" />
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273 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" />
0
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274 </test>
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275 <test>
3
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276 <param name="msgf_input|intype_selector" value="single" />
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277 <param name="msgf_input|s" value="input/201208-378803.mzML" />
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278 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
0
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279 <param name="tda" value="1" />
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280 <param name="t" value="0.02" />
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281 <param name="precursor_ion_tol_units" value="Da" />
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282 <param name="isotope_low" value="-1" />
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283 <param name="isotope_high" value="0" />
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284 <param name="m" value="3" />
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285 <param name="inst" value="2" />
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286 <param name="e" value="3" />
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287 <param name="protocol" value="2" />
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288 <param name="minLength" value="10" />
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289 <param name="maxLength" value="20" />
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290 <param name="minCharge" value="2" />
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291 <param name="maxCharge" value="6" />
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292 <param name="n" value="2" />
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293 <param name="addFeatures" value="1" />
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294
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295 <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" />
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296 <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" />
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297
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298 <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" />
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299 <param name="custom_mods_0|aa_specificity" value="G" />
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300 <param name="custom_mods_0|fix_or_opt" value="opt" />
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301 <param name="custom_mods_0|position_specificity" value="c-term" />
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302 <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" />
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303
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304 <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
2
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305 <param name="custom_mods_1|aa_specificity" value="C,S" />
0
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306 <param name="custom_mods_1|fix_or_opt" value="opt" />
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307 <param name="custom_mods_1|position_specificity" value="any" />
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308 <param name="custom_mods_1|mod_name" value="cGMP" />
6
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309
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310 <output name="output">
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311 <assert_contents>
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312 <has_text text="iTRAQ4plex" />
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313 <has_text text="pyro-Glu" />
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314 <has_text text="Gly-loss" />
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315 <has_text text="cGMP" />
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316 </assert_contents>
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317 </output>
0
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318 </test>
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319 </tests>
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320 <help>
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321 **What it does**
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322
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323 Performs protein identification via database search using MS-GF+.
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324
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325 </help>
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326 <citations>
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327 <citation type="doi">10.1038/ncomms6277</citation>
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328 <citation type="doi">10.1021/pr8001244</citation>
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329 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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330 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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331 </citations>
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332 </tool>