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1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
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2 <description>Run an MSGF+ Search</description>
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3 <requirements>
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4 <requirement type="package" version="1.3">protk</requirement>
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5 <requirement type="package" version="20140210">msgfplus</requirement>
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6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
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7 </requirements>
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8 <command>
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9 msgfplus_search.rb
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10 #if $database.source_select=="built_in":
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11 --galaxy -d $database.dbkey
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12 #else
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13 --galaxy -d $database.fasta_file
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14 #end if
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15
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16 --var-mods='
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17 $variable_mods
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18 #for $custom_variable_mod in $custom_variable_mods:
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19 ,${custom_variable_mod.custom_mod}
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20 #end for
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21 '
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22
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23 --fix-mods='
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24 $fixed_mods
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25 #for $custom_fix_mod in $custom_fix_mods:
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26 ,${custom_fix_mod.custom_mod}
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27 #end for
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28 '
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29
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30 $input_file
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31 -o $output
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32 -r
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33 --enzyme=$enzyme
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34 --precursor-ion-tol-units=$precursor_tolu
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35 -v $missed_cleavages
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36 $cleavage_semi
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37 -p $precursor_ion_tol
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38 --instrument=$instrument
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39 --isotope-error-range=$isotope_error_range
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40 --fragment-method=$fragment_method
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41 --protocol=$protocol
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42 --min-pep-len=$min_pep_len
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43 --max-pep-len=$max_pep_len
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44 --max-pep-charge=$max_pep_charge
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45 --min-pep-charge=$min_pep_charge
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46 --num-reported-matches=$num_reported_matches
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47 --java-mem=$java_mem
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12
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48 #if $pepxml_output_use:
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49 --pepxml
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13
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50 #end if
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10
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51 </command>
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52
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53 <inputs>
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54 <conditional name="database">
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55 <param name="source_select" type="select" label="Database source">
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56 <option value="built_in">Built-In</option>
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57 <option value="input_ref" selected="true">Your Upload File</option>
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58 </param>
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59 <when value="built_in">
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60 <param name="dbkey" type="select" format="text" >
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61 <label>Database</label>
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62 <options from_file="pepxml_databases.loc">
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63 <column name="name" index="0" />
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64 <column name="value" index="2" />
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65 </options>
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66 </param>
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67 </when>
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68 <when value="input_ref">
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69 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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70 </when>
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71 </conditional>
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14
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72 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
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10
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73 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
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74 <options from_file="msgfplus_mods.loc">
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75 <column name="name" index="0" />
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76 <column name="value" index="2" />
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77 </options>
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78 </param>
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79 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
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80 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
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81 <param name="custom_mod" type="text" />
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82 </repeat>
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83 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
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84 <options from_file="msgfplus_mods.loc">
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85 <column name="name" index="0" />
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86 <column name="value" index="2" />
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87 </options>
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88 </param>
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89 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
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90 <param name="custom_mod" type="text">
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91 </param>
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92 </repeat>
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93 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
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94 <label>Missed Cleavages Allowed</label>
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95 <option value="0">0</option>
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96 <option value="1">1</option>
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97 <option value="2">2</option>
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98 </param>
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99
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11
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100 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
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10
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101
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102 <param name="enzyme" type="select" format="text">
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103 <label>Enzyme</label>
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104 <option value="0">unspecific cleavage</option>
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12
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105 <option value="1" selected="true">Trypsin</option>
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106 <option value="2">Chymotrypsin</option>
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107 <option value="3">Lys-C</option>
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108 <option value="4">Lys-N</option>
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109 <option value="5">glutamyl endopeptidase</option>
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110 <option value="6">Arg-C</option>
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111 <option value="7">Asp-N</option>
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112 <option value="8">alphaLP</option>
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113 <option value="9">no cleavage</option>
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114 </param>
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115
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116 <param name="instrument" type="select" format="text">
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117 <label>Instrument Type</label>
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118 <option value="2">TOF</option>
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119 <option value="0">Low-res LCQ/LTQ</option>
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120 <option value="1">High-res LTQ</option>
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121 </param>
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122
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123 <param name="fragment_method" type="select" format="text">
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124 <label>Fragmentation Method</label>
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125 <option value="0">Respect Input File</option>
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126 <option value="1">CID</option>
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127 <option value="2">ETD</option>
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128 <option value="3">HCD</option>
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129 <option value="4">Merge spectra from same precursor</option>
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130 </param>
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131
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132 <param name="protocol" type="select" format="text">
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133 <label>Protocol</label>
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134 <option value="0">NoProtocol</option>
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135 <option value="1">Phosphorylation</option>
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136 <option value="2">iTRAQ</option>
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137 <option value="3">iTRAQPhospho</option>
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138 </param>
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139
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140 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
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141 <param name="precursor_tolu" type="select" format="text">
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142 <label>Precursor Ion Tolerance Units</label>
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143 <option value="ppm">ppm</option>
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144 <option value="Da">Da</option>
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145 </param>
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146
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147 <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/>
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148 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
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149 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
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150 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
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151 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
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152 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
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153 <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
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154 <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
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155 </inputs>
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156 <outputs>
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157 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}">
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158 <change_format>
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159 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"
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160 label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
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161 </change_format>
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162 </data>
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163 </outputs>
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164 <tests>
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165 <test>
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166 <param name="source_select" value="input_ref"/>
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167 <param name="fasta_file" value="bsa.fasta"/>
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168 <param name="input_file" value="bsa.mzML"/>
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169 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" />
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170 </test>
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171 </tests>
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172 <help>
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173
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174 **What it does**
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175
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176 Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
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177
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178 ----
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179
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180 **References**
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181
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182 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
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183
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184 </help>
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185 </tool>
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