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1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
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2
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3 <requirements>
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4 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
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5 <requirement type="package" version="20121116">protk_msgfplus</requirement>
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6 </requirements>
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7
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8
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9 <description>Run an MSGF+ Search</description>
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10
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1
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11
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12
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13 <description>Run an X!Tandem Search</description>
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14
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15 <command>
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16 #if $database.source_select=="built_in":
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17 rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey
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18 #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
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19 #end if
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20
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21
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22 <command>
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23 #if $database.source_select=="built_in":
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24 rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
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25 #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
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0
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26 #end if
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27
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28 --var-mods='
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29 $variable_mods
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30 #for $custom_variable_mod in $custom_variable_mods:
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31 ,${custom_variable_mod.custom_mod}
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32 #end for
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33 '
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34
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35 --fix-mods='
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36 $fixed_mods
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37 #for $custom_fix_mod in $custom_fix_mods:
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38 ,${custom_fix_mod.custom_mod}
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39 #end for
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40 '
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41
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42 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument
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43
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44
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45
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46 </command>
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47
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48 <inputs>
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49 <conditional name="database">
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50 <param name="source_select" type="select" label="Database source">
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51 <option value="built_in">Built-In</option>
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52 <option value="input_ref">Your Upload File</option>
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53 </param>
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54 <when value="built_in">
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55 <param name="dbkey" type="select" format="text" >
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56 <label>Database</label>
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57 <options from_file="pepxml_databases.loc">
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58 <column name="name" index="0" />
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59 <column name="value" index="2" />
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60 </options>
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61 </param>
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62 </when>
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63 <when value="input_ref">
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64 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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65 </when>
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66 </conditional>
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67
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68 <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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69
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70
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71 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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72 clicking to select multiple items">
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73 <options from_file="msgfplus_mods.loc">
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74 <column name="name" index="0" />
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75 <column name="value" index="2" />
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76 </options>
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77 </param>
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78
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79 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
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80 <param name="custom_mod" type="text">
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81 </param>
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82 </repeat>
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83
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84
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85 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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86 clicking to select multiple items">
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87 <options from_file="msgfplus_mods.loc">
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88 <column name="name" index="0" />
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89 <column name="value" index="2" />
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90 </options>
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91 </param>
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92
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93 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
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94 <param name="custom_mod" type="text">
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95 </param>
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96 </repeat>
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97
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98
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99
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100 <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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101 <label>Missed Cleavages Allowed</label>
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102 <option value="0">0</option>
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103 <option value="1">1</option>
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104 <option value="2">2</option>
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105 </param>
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106
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107 <param name="enzyme" type="select" format="text">
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108 <label>Enzyme</label>
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109 <option value="Trypsin">Trypsin</option>
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110 </param>
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111
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112 <param name="instrument" type="select" format="text">
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113 <label>Instrument Type</label>
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114 <option value="2">TOF</option>
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115 <option value="0">Low-res LCQ/LTQ</option>
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116 <option value="1">High-res LTQ</option>
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117 </param>
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118
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119 <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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120
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121 <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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122 <param name="precursor_tolu" type="select" format="text">
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123 <label>Precursor Ion Tolerance Units</label>
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124 <option value="ppm">ppm</option>
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125 <option value="Da">Da</option>
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126 </param>
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127
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128 </inputs>
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129
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130
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131 <outputs>
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132 <data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
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133 </outputs>
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134
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135
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136 <help>
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137
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138 **What it does**
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139
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140 Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
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141
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142 ----
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143
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144 **References**
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145
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146 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
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147
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148 </help>
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149
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150 </tool>
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