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1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0">
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2
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.1</container>
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5 <requirement type="package" version="1.4">protk</requirement>
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6 </requirements>
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7
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8 <description>Mascot MS/MS Search</description>
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9
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10
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11 <command>mascot_search.rb
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12
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13 #if $database.source_select=="built_in":
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14 -d $database.dbkey
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15 #else
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16 -d $database.custom_db
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17 #end if
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18
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19 -f $fragment_ion_tol
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20
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21 -S $server $input_file
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22
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23 -o $output
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24
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25 -r
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26
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27 ## Variable Mods
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28
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29 --var-mods='
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30 $variable_mods
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31 '
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32
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33 --fix-mods='
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34 $fixed_mods
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35 '
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36
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37 --allowed-charges='$allowed_charges'
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38
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39 --enzyme=$enzyme
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40
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41 --instrument='$instrument'
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42
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43 -p $precursor_ion_tol
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44
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45 --precursor-ion-tol-units=$precursor_tolu
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46
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47 #if $email
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48 --email=$email
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49 #end if
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50
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51 -v $missed_cleavages
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52
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53 --quantitation='$quant_method'
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54
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55 #if $security.security_use
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56 --use-security
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57 --username $security.username
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58 --password $security.password
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59 #end if
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60
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61 #if $proxy
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62 --proxy $proxy
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63 #end if
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64
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65 --timeout=600
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66
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67 </command>
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68
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69 <inputs>
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70
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71 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
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72
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73 <conditional name="database">
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74 <param name="source_select" type="select" label="Database Type">
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75 <option value="built_in">Built-In</option>
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76 <option selected="true" value="custom_defined">Custom</option>
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77 </param>
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78 <when value="built_in">
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79 <param name="dbkey" type="select" format="text" >
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80 <label>Database</label>
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81 <options from_file="mascot_databases.loc">
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82 <column name="name" index="0" />
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83 <column name="value" index="2" />
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84 </options>
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85 </param>
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86 </when>
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87 <when value="custom_defined">
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88 <param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
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89 </when>
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90 </conditional>
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91
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92 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
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93 <options from_file="mascot_mods.loc">
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94 <column name="name" index="0" />
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95 <column name="value" index="2" />
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96 </options>
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97 </param>
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98
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99 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
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100 <options from_file="mascot_mods.loc">
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101 <column name="name" index="0" />
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102 <column name="value" index="2" />
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103 </options>
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104 </param>
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105
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106 <param name="missed_cleavages" type="select" format="text">
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107 <label>Missed Cleavages Allowed</label>
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108 <option value="0">0</option>
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109 <option value="1">1</option>
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110 <option selected="true" value="2">2</option>
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111 </param>
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112
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113 <param name="enzyme" type="select" format="text">
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114 <label>Enzyme</label>
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115 <option selected="true" value="Trypsin">Trypsin</option>
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116 <option value="Trypsin/P">Trypsin/P</option>
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117 <option value="Arg-C">Arg-C</option>
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118 <option value="Asp-N">Asp-N</option>
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119 <option value="Asp-N_ambic">Asp-N_ambic</option>
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120 <option value="Chymotrypsin">Chymotrypsin</option>
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121 <option value="CNBr">CNBr</option>
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122 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
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123 <option value="Formic_acid">Formic_acid</option>
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124 <option value="Lys-C">Lys-C</option>
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125 <option value="Lys-C/P">Lys-C/P</option>
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126 <option value="LysC+AspN">LysC+AspN</option>
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127 <option value="Lys-N">Lys-N</option>
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128 <option value="PepsinA">PepsinA</option>
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129 <option value="semiTrypsin">semiTrypsin</option>
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130 <option value="TrypChymo">TrypChymo</option>
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131 <option value="TrypsinMSIPI">TrypsinMSIPI</option>
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132 <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
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133 <option value="V8-DE">V8-DE</option>
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134 <option value="V8-E">V8-E</option>
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135 <option value="none">none</option>
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136 </param>
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137
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138 <param name="allowed_charges" type="select" format="text">
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139 <label>Peptide Charge</label>
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140 <option value="8-">8-</option>
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141 <option value="7-">7-</option>
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142 <option value="6-">6-</option>
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143 <option value="5-">5-</option>
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144 <option value="4-">4-</option>
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145 <option value="3-">3-</option>
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146 <option value="2-,3- and 4-">2-,3- and 4-</option>
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147 <option value="2- and 3-">2- and 3-</option>
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148 <option value="2-">2-</option>
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149 <option value="1-,2- and 3-">1-,2- and 3-</option>
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150 <option value="1-">1-</option>
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151 <option value="Mr">Mr</option>
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152 <option value="1+">1+</option>
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153 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
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154 <option value="2+">2+</option>
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155 <option value="2+ and 3+">2+ and 3+</option>
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156 <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
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157 <option value="3+">3+</option>
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158 <option value="4+">4+</option>
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159 <option value="5+">5+</option>
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160 <option value="6+">6+</option>
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161 <option value="7+">7+</option>
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162 <option value="8+">8+</option>
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163 </param>
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164
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165 <param name="instrument" type="select" format="text">
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166 <label>Instrument</label>
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167 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
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168 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
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169 <option selected="true" value="ESI-TRAP">ESI-TRAP</option>
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170 <option value="ESI-QUAD">ESI-QUAD</option>
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171 <option value="ESI-FTICR">ESI-FTICR</option>
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172 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
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173 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
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174 <option value="FTMS-ECD">FTMS-ECD</option>
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175 <option value="ETD-TRAP">ETD-TRAP</option>
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176 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
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177 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
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178 <option value="MALDI-ISD">MALDI-ISD</option>
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179 <option value="CID+ETD">CID+ETD</option>
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180 </param>
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181
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182
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183 <param name="quant_method" type="select" format="text">
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184 <label>Quantitation</label>
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185 <option selected="true" value="None">None</option>
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186 <option value="iTRAQ 4plex">iTRAQ 4plex</option>
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187 <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
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188 <option value="iTRAQ 8plex">iTRAQ 8plex</option>
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189 <option value="TMT 6plex">TMT 6plex</option>
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190 <option value="TMT 2plex">TMT 2plex</option>
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191 <option value="DiLeu 4plex">DiLeu 4plex</option>
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192 <option value="18O multiplex">18O multiplex</option>
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193 <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
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194 <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
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195 <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
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196 <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
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197 <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
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198 <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
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199 <option value="18O corrected [MD]">18O corrected [MD]</option>
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200 <option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
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201 <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
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202 <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
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203 <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
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204 <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
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205 <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
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206 <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>
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207 <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
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208 <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
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209 <option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
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210 <option value="Dimethylation [MD]">Dimethylation [MD]</option>
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211 <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
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212 <option value="Acetylation [MD]">Acetylation [MD]</option>
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213 <option value="Label-free [MD]">Label-free [MD]</option>
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214 </param>
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215
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216 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
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217
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218 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
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219 <param name="precursor_tolu" type="select" format="text">
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220 <label>Precursor Ion Tolerance Units</label>
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221 <option value="ppm">ppm</option>
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222 <option value="Da">Da</option>
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223 </param>
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224
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225 <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
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226 <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
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227
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228 <conditional name="security">
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229 <param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
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230 <when value="false" />
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231 <when value="true">
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232 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
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233 <param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
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234 </when>
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235 </conditional>
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236 <param name="email" type="text" label="Email " size="60" value="" help=""/>
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237
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238
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239
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240 </inputs>
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241 <outputs>
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242 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
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243 </outputs>
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244
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245 <help>
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246 Run a Mascot MS/MS Ion Search
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247 </help>
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248
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249 </tool>
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