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1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.0">
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2
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3
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4 <requirements>
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5 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
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6 </requirements>
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7
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8 <description>Run a Mascot Search on a File</description>
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9
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10
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11 <command>rvm 1.9.3@protk-1.1.9 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
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12 ## Variable Mods
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13
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14 --var-mods='
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15 $variable_mods
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16 '
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17
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18 --fix-mods='
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19 $fixed_mods
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20 '
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21 --allowed-charges=$allowed_charges --enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages
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22
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23 </command>
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24
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25 <inputs>
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26
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27 <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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28
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29 <param name="database" type="select" format="text" >
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30 <label>Database</label>
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31 <options from_file="mascot_databases.loc">
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32 <column name="name" index="0" />
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33 <column name="value" index="2" />
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34 </options>
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35 </param>
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36
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37
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38
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39 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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40 clicking to select multiple items">
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41 <options from_file="mascot_mods.loc">
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42 <column name="name" index="0" />
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43 <column name="value" index="2" />
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44 </options>
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45 </param>
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46
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47 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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48 clicking to select multiple items">
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49 <options from_file="mascot_mods.loc">
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50 <column name="name" index="0" />
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51 <column name="value" index="2" />
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52 </options>
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53 </param>
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54
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55 <param name="missed_cleavages" type="select" format="text">
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56 <label>Missed Cleavages Allowed</label>
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57 <option value="0">0</option>
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58 <option value="1">1</option>
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59 <option value="2">2</option>
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60 </param>
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61
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62 <param name="enzyme" type="select" format="text">
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63 <label>Enzyme</label>
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64 <option value="Trypsin">Trypsin</option>
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65 </param>
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66
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67 <param name="allowed_charges" type="select" format="text">
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68 <label>Peptide Charge</label>
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69 <option value="8-">8-</option>
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70 <option value="7-">7-</option>
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71 <option value="6-">6-</option>
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72 <option value="5-">5-</option>
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73 <option value="4-">4-</option>
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74 <option value="3-">3-</option>
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75 <option value="2-,3- and 4-">2-,3- and 4-</option>
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76 <option value="2- and 3-">2- and 3-</option>
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77 <option value="2-">2-</option>
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78 <option value="1-,2- and 3-">1-,2- and 3-</option>
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79 <option value="1-">1-</option>
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80 <option value="Mr">Mr</option>
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81 <option value="1+">1+</option>
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82 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
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83 <option value="2+">2+</option>
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84 <option value="2+ and 3+">2+ and 3+</option>
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85 <option value="2+,3+ and 4+">2+,3+ and 4+</option>
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86 <option value="3+">3+</option>
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87 <option value="4+">4+</option>
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88 <option value="5+">5+</option>
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89 <option value="6+">6+</option>
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90 <option value="7+">7+</option>
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91 <option value="8+">8+</option>
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92 </param>
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93
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94 <param name="instrument" type="select" format="text">
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95 <label>Instrument</label>
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96 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
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97 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
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98 <option value="ESI-TRAP">ESI-TRAP</option>
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99 <option value="ESI-QUAD">ESI-QUAD</option>
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100 <option value="ESI-FTICR">ESI-FTICR</option>
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101 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
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102 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
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103 <option value="FTMS-ECD">FTMS-ECD</option>
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104 <option value="ETD-TRAP">ETD-TRAP</option>
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105 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
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106 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
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107 <option value="MALDI-ISD">MALDI-ISD</option>
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108 <option value="CID+ETD">CID+ETD</option>
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109 </param>
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110
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111 <param name="fragment_ion_tol" label="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
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112
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113 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Precursor ion tolerance"/>
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114 <param name="precursor_tolu" type="select" format="text">
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115 <label>Precursor Ion Tolerance Units</label>
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116 <option value="ppm">ppm</option>
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117 <option value="Da">Da</option>
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118 </param>
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119
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120 <param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
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121
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122 <param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/>
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123
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124 <param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/>
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125
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126 </inputs>
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127 <outputs>
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128 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/>
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129 </outputs>
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130
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131 <help>
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132 Run a Mascot Search
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133 </help>
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134
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135 </tool>
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