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1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1">
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4 <requirements>
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5
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5 <requirement type="package" version="1.2.2">galaxy_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>rvm 1.9.3@protk-1.2.2 do 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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2
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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 $fixed_mods
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35 '
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36 --allowed-charges=$allowed_charges
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37
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38 --enzyme=$enzyme
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39
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40 --instrument=$instrument
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41
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42 --precursor-ion-tol-units=$precursor_tolu
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43
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44 --email=$email
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45
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46 -v $missed_cleavages
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47
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48 #if $security.security_use
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49 --use-security
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50 --username $security.username
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51 --password $security.password
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52 #end if
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53
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54 #if $proxy
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55 --proxy $proxy
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56 #end if
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57
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58 </command>
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59
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60 <inputs>
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61
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62 <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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63
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64 <conditional name="database">
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65 <param name="source_select" type="select" label="Database Type">
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66 <option value="built_in">Built-In</option>
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67 <option value="custom_defined">Custom</option>
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68 </param>
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69 <when value="built_in">
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70 <param name="dbkey" type="select" format="text" >
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71 <label>Database</label>
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72 <options from_file="mascot_databases.loc">
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73 <column name="name" index="0" />
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74 <column name="value" index="2" />
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75 </options>
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76 </param>
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77 </when>
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78 <when value="custom_defined">
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79 <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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80 </when>
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81 </conditional>
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82
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83 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
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84 <options from_file="mascot_mods.loc">
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85 <column name="name" index="0" />
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86 <column name="value" index="2" />
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87 </options>
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88 </param>
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89
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90 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
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91 <options from_file="mascot_mods.loc">
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92 <column name="name" index="0" />
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93 <column name="value" index="2" />
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94 </options>
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95 </param>
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96
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97 <param name="missed_cleavages" type="select" format="text">
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98 <label>Missed Cleavages Allowed</label>
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99 <option value="0">0</option>
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100 <option value="1">1</option>
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101 <option value="2">2</option>
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102 </param>
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103
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104 <param name="enzyme" type="select" format="text">
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105 <label>Enzyme</label>
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106 <option value="Trypsin">Trypsin</option>
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107 </param>
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108
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109 <param name="allowed_charges" type="select" format="text">
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110 <label>Peptide Charge</label>
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111 <option value="8-">8-</option>
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112 <option value="7-">7-</option>
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113 <option value="6-">6-</option>
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114 <option value="5-">5-</option>
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115 <option value="4-">4-</option>
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116 <option value="3-">3-</option>
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117 <option value="2-,3- and 4-">2-,3- and 4-</option>
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118 <option value="2- and 3-">2- and 3-</option>
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119 <option value="2-">2-</option>
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120 <option value="1-,2- and 3-">1-,2- and 3-</option>
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121 <option value="1-">1-</option>
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122 <option value="Mr">Mr</option>
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123 <option value="1+">1+</option>
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124 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
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125 <option value="2+">2+</option>
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126 <option value="2+ and 3+">2+ and 3+</option>
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127 <option value="2+,3+ and 4+">2+,3+ and 4+</option>
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128 <option value="3+">3+</option>
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129 <option value="4+">4+</option>
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130 <option value="5+">5+</option>
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131 <option value="6+">6+</option>
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132 <option value="7+">7+</option>
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133 <option value="8+">8+</option>
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134 </param>
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135
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136 <param name="instrument" type="select" format="text">
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137 <label>Instrument</label>
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138 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
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139 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
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140 <option value="ESI-TRAP">ESI-TRAP</option>
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141 <option value="ESI-QUAD">ESI-QUAD</option>
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142 <option value="ESI-FTICR">ESI-FTICR</option>
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143 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
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144 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
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145 <option value="FTMS-ECD">FTMS-ECD</option>
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146 <option value="ETD-TRAP">ETD-TRAP</option>
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147 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
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148 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
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149 <option value="MALDI-ISD">MALDI-ISD</option>
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150 <option value="CID+ETD">CID+ETD</option>
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151 </param>
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152
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153 <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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154
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155 <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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156 <param name="precursor_tolu" type="select" format="text">
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157 <label>Precursor Ion Tolerance Units</label>
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158 <option value="ppm">ppm</option>
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159 <option value="Da">Da</option>
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160 </param>
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161
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162 <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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163 <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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164
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165 <conditional name="security">
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166 <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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167 <when value="false" />
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168 <when value="true">
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169 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
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170 <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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171 </when>
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172 </conditional>
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173 <param name="email" type="text" label="Email " size="60" value="" help=""/>
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174
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175
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176
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177 </inputs>
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178 <outputs>
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179 <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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180 </outputs>
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181
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182 <help>
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183 Run a Mascot Search
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184 </help>
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185
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186 </tool>
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