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1 <tool id="proteomics_search_mascot_1" name="Mascot 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">protk</requirement>
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5 </requirements>
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6
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7 <description>Mascot MS/MS Search</description>
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8
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9
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10 <command>mascot_search.rb
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11
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12 #if $database.source_select=="built_in":
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13 -d $database.dbkey
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14 #else
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15 -d $database.custom_db
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16 #end if
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17
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18 -f $fragment_ion_tol
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19
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20 -S $server $input_file
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21
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22 -o $output
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23
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24 -r
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25
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26 ## Variable Mods
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27
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28 --var-mods='
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29 $variable_mods
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30 '
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31
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32 --fix-mods='
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33 $fixed_mods
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34 '
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35 --allowed-charges=$allowed_charges
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36
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37 --enzyme=$enzyme
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38
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39 --instrument=$instrument
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40
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41 --precursor-ion-tol-units=$precursor_tolu
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42
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43 --email=$email
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44
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45 -v $missed_cleavages
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46
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47 #if $security.security_use
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48 --use-security
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49 --username $security.username
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50 --password $security.password
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51 #end if
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52
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53 #if $proxy
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54 --proxy $proxy
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55 #end if
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56
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57 </command>
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58
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59 <inputs>
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60
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61 <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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62
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63 <conditional name="database">
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64 <param name="source_select" type="select" label="Database Type">
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65 <option value="built_in">Built-In</option>
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66 <option value="custom_defined">Custom</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="mascot_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="custom_defined">
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78 <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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79 </when>
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80 </conditional>
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81
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82 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
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83 <options from_file="mascot_mods.loc">
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84 <column name="name" index="0" />
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85 <column name="value" index="2" />
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86 </options>
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87 </param>
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88
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89 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
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90 <options from_file="mascot_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 <param name="missed_cleavages" type="select" format="text">
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97 <label>Missed Cleavages Allowed</label>
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98 <option value="0">0</option>
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99 <option value="1">1</option>
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100 <option value="2">2</option>
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101 </param>
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102
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103 <param name="enzyme" type="select" format="text">
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104 <label>Enzyme</label>
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105 <option value="Trypsin">Trypsin</option>
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106 <option value="Trypsin/P">Trypsin/P</option>
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107 <option value="Arg-C">Arg-C</option>
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108 <option value="Asp-N">Asp-N</option>
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109 <option value="Asp-N_ambic">Asp-N_ambic</option>
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110 <option value="Chymotrypsin">Chymotrypsin</option>
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111 <option value="CNBr">CNBr</option>
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112 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
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113 <option value="Formic_acid">Formic_acid</option>
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114 <option value="Lys-C">Lys-C</option>
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115 <option value="Lys-C/P">Lys-C/P</option>
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116 <option value="LysC+AspN">LysC+AspN</option>
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117 <option value="Lys-N">Lys-N</option>
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118 <option value="PepsinA">PepsinA</option>
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119 <option value="semiTrypsin">semiTrypsin</option>
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120 <option value="TrypChymo">TrypChymo</option>
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121 <option value="TrypsinMSIPI">TrypsinMSIPI</option>
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122 <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
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123 <option value="V8-DE">V8-DE</option>
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124 <option value="V8-E">V8-E</option>
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125 <option value="none">none</option>
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126 </param>
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127
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128 <param name="allowed_charges" type="select" format="text">
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129 <label>Peptide Charge</label>
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130 <option value="8-">8-</option>
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131 <option value="7-">7-</option>
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132 <option value="6-">6-</option>
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133 <option value="5-">5-</option>
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134 <option value="4-">4-</option>
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135 <option value="3-">3-</option>
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136 <option value="2-,3- and 4-">2-,3- and 4-</option>
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137 <option value="2- and 3-">2- and 3-</option>
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138 <option value="2-">2-</option>
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139 <option value="1-,2- and 3-">1-,2- and 3-</option>
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140 <option value="1-">1-</option>
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141 <option value="Mr">Mr</option>
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142 <option value="1+">1+</option>
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143 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
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144 <option value="2+">2+</option>
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145 <option value="2+ and 3+">2+ and 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="3+">3+</option>
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148 <option value="4+">4+</option>
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149 <option value="5+">5+</option>
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150 <option value="6+">6+</option>
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151 <option value="7+">7+</option>
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152 <option value="8+">8+</option>
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153 </param>
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154
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155 <param name="instrument" type="select" format="text">
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156 <label>Instrument</label>
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157 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
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158 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
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159 <option value="ESI-TRAP">ESI-TRAP</option>
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160 <option value="ESI-QUAD">ESI-QUAD</option>
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161 <option value="ESI-FTICR">ESI-FTICR</option>
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162 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
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163 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
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164 <option value="FTMS-ECD">FTMS-ECD</option>
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165 <option value="ETD-TRAP">ETD-TRAP</option>
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166 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
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167 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
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168 <option value="MALDI-ISD">MALDI-ISD</option>
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169 <option value="CID+ETD">CID+ETD</option>
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170 </param>
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171
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172 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
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173
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174 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
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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="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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182 <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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183
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184 <conditional name="security">
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185 <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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186 <when value="false" />
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187 <when value="true">
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188 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
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189 <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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190 </when>
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191 </conditional>
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192 <param name="email" type="text" label="Email " size="60" value="" help=""/>
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193
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194
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195
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196 </inputs>
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197 <outputs>
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198 <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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199 </outputs>
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200
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201 <help>
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202 Run a Mascot MS/MS Ion Search
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203 </help>
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204
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205 </tool>
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