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1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.4">
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2
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3 <requirements>
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4 <container type="docker">simonalpha/protk:1.4.0</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>Run an X!Tandem Search</description>
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9
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10 <command>
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11 #if $database.source_select=="built_in":
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12 tandem_search.rb -d $database.dbkey
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13 #else
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14 tandem_search.rb -d $database.fasta_file
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15 #end if
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16
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17 #if $tandem_params.source_select=="built_in":
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18 -T $tandem_params.paramskey
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19 #else
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20 -T $tandem_params.params_file
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21 #end if
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22
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23
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24 --var-mods='
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25 $variable_mods
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26 #for $custom_variable_mod in $custom_variable_mods:
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27 ,${custom_variable_mod.custom_mod}
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28 #end for
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29 '
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30
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31 --fix-mods='
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32 $fixed_mods
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33 #for $custom_fix_mod in $custom_fix_mods:
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34 ,${custom_fix_mod.custom_mod}
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35 #end for
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36 '
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37
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38 $input_file -o $output -r
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39
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40 --enzyme=$enzyme
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41
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42 --precursor-ion-tol-units=$precursor_tolu
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43
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44 -v $missed_cleavages
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45
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46 -f $fragment_ion_tol
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47
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48 -p $precursor_ion_tol
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49
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50 $allow_multi_isotope_search
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51
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52 $acetyl_protein_nterm
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53
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54 $cleavage_semi
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55
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56 $keep_spectra
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57
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58 --threads $threads
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59
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60 </command>
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61
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62 <inputs>
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63 <conditional name="database">
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64 <param name="source_select" type="select" label="Database source">
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65 <option value="built_in">Built-In</option>
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66 <option value="input_ref" selected="true">Your Upload File</option>
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67 </param>
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68 <when value="built_in">
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69 <param name="dbkey" type="select" format="text" >
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70 <label>Database</label>
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71 <options from_file="pepxml_databases.loc">
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72 <column name="name" index="0" />
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73 <column name="value" index="2" />
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74 </options>
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75 </param>
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76 </when>
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77 <when value="input_ref">
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78 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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79 </when>
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80 </conditional>
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81
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82 <conditional name="tandem_params">
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83 <param name="source_select" type="select" label="Baseline Parameters">
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84 <option value="built_in" selected="true">Built-In</option>
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85 <option value="input_ref">Custom parameter file</option>
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86 </param>
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87 <when value="built_in">
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88 <param name="paramskey" type="select" format="text" >
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89 <label>Paramset</label>
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90 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
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91 <option value="isb_native">ISB Native</option>
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92 <option value="gpm">GPM</option>
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93 </param>
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94 </when>
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95 <when value="input_ref">
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96 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
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97 </when>
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98 </conditional>
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99
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100 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
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101
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102 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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103 clicking to select multiple items">
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104 <options from_file="tandem_mods.loc">
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105 <column name="name" index="0" />
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106 <column name="value" index="2" />
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107 </options>
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108 </param>
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109
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110 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
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111 <param name="custom_mod" type="text">
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112 </param>
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113 </repeat>
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114
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115
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116 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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117 clicking to select multiple items">
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118 <options from_file="tandem_mods.loc">
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119 <column name="name" index="0" />
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120 <column name="value" index="2" />
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121 </options>
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122 </param>
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123
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124 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
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125 <param name="custom_mod" type="text">
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126 </param>
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127 </repeat>
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128
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129 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
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130
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131
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132 <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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133 <label>Missed Cleavages Allowed</label>
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134 <option value="0">0</option>
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135 <option value="1">1</option>
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136 <option selected="true" value="2">2</option>
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137 </param>
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138
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139 <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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140
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141 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
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142
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143 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
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144
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145 <param name="enzyme" type="select" format="text">
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146 <label>Enzyme</label>
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147 <option value="[R]__pc__{P}">argc - [R]|{P}</option>
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148 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
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149 <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
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150 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
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151 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
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152 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
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153 <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
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154 <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
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155 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
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156 <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
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157 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
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158 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
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159 <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
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160 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
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161 <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
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162 <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
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163 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
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164 <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
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165 <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
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166 <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
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167 <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
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168 <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
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169 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
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170 </param>
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171
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172
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173 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
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174
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175 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
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176 <param name="precursor_tolu" type="select" format="text">
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177 <label>Precursor Ion Tolerance Units</label>
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178 <option value="ppm">ppm</option>
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179 <option value="Da">Da</option>
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180 </param>
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181
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182 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
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183
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184 </inputs>
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185
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186
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187 <outputs>
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188 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
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189 </outputs>
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190
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191
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192 <help>
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193
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194 **What it does**
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195
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196 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
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197
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198 ----
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199
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200 **References**
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201
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202 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
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203
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204 </help>
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205
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206 </tool>
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