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1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2">
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2
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3 <requirements>
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4 <requirement type="package" version="1.3.0">protk</requirement>
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5 </requirements>
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6
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7 <description>Run an X!Tandem Search</description>
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8
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9 <command>
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10 #if $database.source_select=="built_in":
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11 tandem_search.rb -d $database.dbkey
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12 #else
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13 tandem_search.rb -d $database.fasta_file
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14 #end if
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15
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16 #if $tandem_params.source_select=="built_in":
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17 -T $tandem_params.paramskey
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18 #else
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19 -T $tandem_params.params_file
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20 #end if
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21
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22
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23 --var-mods='
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24 $variable_mods
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25 #for $custom_variable_mod in $custom_variable_mods:
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26 ,${custom_variable_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 --fix-mods='
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31 $fixed_mods
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32 #for $custom_fix_mod in $custom_fix_mods:
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33 ,${custom_fix_mod.custom_mod}
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34 #end for
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35 '
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36
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37 $input_file -o $output -r
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38
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39 --enzyme=$enzyme
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40
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41 --precursor-ion-tol-units=$precursor_tolu
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42
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43 -v $missed_cleavages
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44
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45 -f $fragment_ion_tol
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46
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47 -p $precursor_ion_tol
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48
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49 $allow_multi_isotope_search
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50
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51 $acetyl_protein_nterm
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52
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53 $cleavage_semi
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54
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55 $keep_spectra
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56
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57 --threads $threads
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58
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59 </command>
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60
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61 <inputs>
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62 <conditional name="database">
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63 <param name="source_select" type="select" label="Database source">
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64 <option value="built_in">Built-In</option>
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65 <option value="input_ref" selected="true">Your Upload File</option>
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66 </param>
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67 <when value="built_in">
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68 <param name="dbkey" type="select" format="text" >
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69 <label>Database</label>
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70 <options from_file="pepxml_databases.loc">
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71 <column name="name" index="0" />
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72 <column name="value" index="2" />
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73 </options>
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74 </param>
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75 </when>
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76 <when value="input_ref">
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77 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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78 </when>
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79 </conditional>
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80
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81 <conditional name="tandem_params">
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82 <param name="source_select" type="select" label="Baseline Parameters">
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83 <option value="built_in" selected="true">Built-In</option>
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84 <option value="input_ref">Custom parameter file</option>
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85 </param>
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86 <when value="built_in">
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87 <param name="paramskey" type="select" format="text" >
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88 <label>Paramset</label>
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13
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89 <option value="gpm">GPM</option>
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90 <option value="isb_native">ISB Native</option>
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91 <option value="isb_kscore">ISB K-Score</option>
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92 </param>
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93 </when>
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94 <when value="input_ref">
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95 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
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96 </when>
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97 </conditional>
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98
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99 <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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100
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101 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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102 clicking to select multiple items">
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103 <options from_file="tandem_mods.loc">
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104 <column name="name" index="0" />
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105 <column name="value" index="2" />
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106 </options>
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107 </param>
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108
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109 <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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110 <param name="custom_mod" type="text">
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111 </param>
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112 </repeat>
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113
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114
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115 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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116 clicking to select multiple items">
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117 <options from_file="tandem_mods.loc">
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118 <column name="name" index="0" />
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119 <column name="value" index="2" />
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120 </options>
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121 </param>
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122
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123 <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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124 <param name="custom_mod" type="text">
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125 </param>
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126 </repeat>
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127
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128 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
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129
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130
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131 <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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132 <label>Missed Cleavages Allowed</label>
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133 <option value="0">0</option>
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134 <option value="1">1</option>
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135 <option value="2">2</option>
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136 </param>
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137
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138 <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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139
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140 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
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141
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142 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
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143
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144 <param name="enzyme" type="select" format="text">
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145 <label>Enzyme</label>
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146 <option value="[R]|{P}">argc - [R]|{P}</option>
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147 <option value="[X]|[D]">aspn - [X]|[D]</option>
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148 <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>
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149 <option value="[R]|[X]">clostripain - [R]|[X]</option>
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150 <option value="[M]|{P}">cnbr - [M]|{P}</option>
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151 <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>
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152 <option value="[D]|{P}">formicacid - [D]|{P}</option>
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153 <option value="[DE]|{P}">gluc - [DE]|{P}</option>
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154 <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>
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155 <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>
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156 <option value="[K]|{P}">lysc - [K]|{P}</option>
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157 <option value="[K]|[X]">lysc-p - [K]|[X]</option>
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158 <option value="[X]|[K]">lysn - [X]|[K]</option>
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159 <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>
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160 <option value="[X]|[X]">nonspecific - [X]|[X]</option>
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161 <option value="[FL]|[X]">pepsina - [FL]|[X]</option>
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162 <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>
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163 <option value="[E]|[X]">staph_protease - [E]|[X]</option>
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164 <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
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165 <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>
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166 <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
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167 <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
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168 <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option>
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169 </param>
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170
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171
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172 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
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173
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174 <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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175 <param name="precursor_tolu" type="select" format="text">
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176 <label>Precursor Ion Tolerance Units</label>
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177 <option value="ppm">ppm</option>
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178 <option value="Da">Da</option>
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179 </param>
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180
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181 <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="" falsevalue=""/>
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182
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183 </inputs>
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184
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185
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186 <outputs>
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187 <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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188 </outputs>
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189
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190
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191 <help>
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192
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193 **What it does**
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194
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195 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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196
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197 ----
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198
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199 **References**
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200
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201 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
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202
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203 </help>
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204
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205 </tool>
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