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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="1.2.6">protk</requirement>
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5 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</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 --var-mods='
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18 $variable_mods
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19 #for $custom_variable_mod in $custom_variable_mods:
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20 ,${custom_variable_mod.custom_mod}
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21 #end for
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22 '
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23
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24 --fix-mods='
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25 $fixed_mods
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26 #for $custom_fix_mod in $custom_fix_mods:
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27 ,${custom_fix_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 $input_file -o $output -r
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32
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33 --enzyme=$enzyme
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34
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35 --precursor-ion-tol-units=$precursor_tolu
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36
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37 -v $missed_cleavages
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38
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39 -f $fragment_ion_tol
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40
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41 -p $precursor_ion_tol
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42
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43 $allow_multi_isotope_search
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44
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45 --keep-params-files
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46
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47 $cleavage_semi
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48
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49 </command>
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50
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51 <inputs>
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52 <conditional name="database">
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53 <param name="source_select" type="select" label="Database source">
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54 <option value="built_in">Built-In</option>
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55 <option value="input_ref" selected="true">Your Upload File</option>
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56 </param>
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57 <when value="built_in">
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58 <param name="dbkey" type="select" format="text" >
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59 <label>Database</label>
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60 <options from_file="pepxml_databases.loc">
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61 <column name="name" index="0" />
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62 <column name="value" index="2" />
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63 </options>
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64 </param>
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65 </when>
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66 <when value="input_ref">
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67 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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68 </when>
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69 </conditional>
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70
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71 <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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72
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73
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74 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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75 clicking to select multiple items">
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76 <options from_file="tandem_mods.loc">
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77 <column name="name" index="0" />
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78 <column name="value" index="2" />
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79 </options>
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80 </param>
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81
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82 <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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83 <param name="custom_mod" type="text">
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84 </param>
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85 </repeat>
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86
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87
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88 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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89 clicking to select multiple items">
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90 <options from_file="tandem_mods.loc">
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91 <column name="name" index="0" />
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92 <column name="value" index="2" />
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93 </options>
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94 </param>
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95
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96 <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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97 <param name="custom_mod" type="text">
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98 </param>
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99 </repeat>
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100
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101
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102
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103 <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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104 <label>Missed Cleavages Allowed</label>
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105 <option value="0">0</option>
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106 <option value="1">1</option>
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107 <option value="2">2</option>
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108 </param>
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109
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110 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
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111
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112 <param name="enzyme" type="select" format="text">
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113 <label>Enzyme</label>
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114 <option value="[R]|{P}">argc - [R]|{P}</option>
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115 <option value="[X]|[D]">aspn - [X]|[D]</option>
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116 <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>
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117 <option value="[R]|[X]">clostripain - [R]|[X]</option>
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118 <option value="[M]|{P}">cnbr - [M]|{P}</option>
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119 <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>
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120 <option value="[D]|{P}">formicacid - [D]|{P}</option>
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121 <option value="[DE]|{P}">gluc - [DE]|{P}</option>
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122 <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>
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123 <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>
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124 <option value="[K]|{P}">lysc - [K]|{P}</option>
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125 <option value="[K]|[X]">lysc-p - [K]|[X]</option>
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126 <option value="[X]|[K]">lysn - [X]|[K]</option>
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127 <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>
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128 <option value="[X]|[X]">nonspecific - [X]|[X]</option>
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129 <option value="[FL]|[X]">pepsina - [FL]|[X]</option>
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130 <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>
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131 <option value="[E]|[X]">staph_protease - [E]|[X]</option>
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132 <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
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133 <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>
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134 <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
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135 <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
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136 <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option>
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137 </param>
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138
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139
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140 <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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141
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142 <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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143 <param name="precursor_tolu" type="select" format="text">
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144 <label>Precursor Ion Tolerance Units</label>
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145 <option value="ppm">ppm</option>
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146 <option value="Da">Da</option>
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147 </param>
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148
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149 <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="--strict-monoisotopic-mass"/>
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150
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151 </inputs>
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152
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153
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154 <outputs>
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155 <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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156 </outputs>
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157
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158
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159 <help>
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160
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161 **What it does**
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162
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163 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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164
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165 ----
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166
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167 **References**
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168
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169 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
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170
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171 </help>
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172
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173 </tool>
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