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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">msgfplus</requirement>
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6 <package name="proteowizard" version="3_0_4388">
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7 </requirements>
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8
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9
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10 <description>Run an MSGF+ Search</description>
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11
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12 <command>
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13 #if $database.source_select=="built_in":
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14 rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
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15 #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
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16 #end if
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17
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18 --var-mods='
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19 $variable_mods
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20 #for $custom_variable_mod in $custom_variable_mods:
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21 ,${custom_variable_mod.custom_mod}
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22 #end for
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23 '
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24
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25 --fix-mods='
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26 $fixed_mods
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27 #for $custom_fix_mod in $custom_fix_mods:
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28 ,${custom_fix_mod.custom_mod}
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29 #end for
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30 '
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31
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32 $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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33
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34
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35
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36 </command>
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37
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38 <inputs>
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39 <conditional name="database">
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40 <param name="source_select" type="select" label="Database source">
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41 <option value="built_in">Built-In</option>
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42 <option value="input_ref">Your Upload File</option>
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43 </param>
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44 <when value="built_in">
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45 <param name="dbkey" type="select" format="text" >
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46 <label>Database</label>
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47 <options from_file="pepxml_databases.loc">
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48 <column name="name" index="0" />
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49 <column name="value" index="2" />
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50 </options>
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51 </param>
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52 </when>
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53 <when value="input_ref">
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54 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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55 </when>
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56 </conditional>
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57
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58 <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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59
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60
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61 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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62 clicking to select multiple items">
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63 <options from_file="msgfplus_mods.loc">
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64 <column name="name" index="0" />
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65 <column name="value" index="2" />
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66 </options>
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67 </param>
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68
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69 <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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70 <param name="custom_mod" type="text">
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71 </param>
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72 </repeat>
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73
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74
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75 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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76 clicking to select multiple items">
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77 <options from_file="msgfplus_mods.loc">
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78 <column name="name" index="0" />
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79 <column name="value" index="2" />
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80 </options>
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81 </param>
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82
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83 <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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84 <param name="custom_mod" type="text">
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85 </param>
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86 </repeat>
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87
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88
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89
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90 <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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91 <label>Missed Cleavages Allowed</label>
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92 <option value="0">0</option>
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93 <option value="1">1</option>
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94 <option value="2">2</option>
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95 </param>
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96
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97 <param name="enzyme" type="select" format="text">
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98 <label>Enzyme</label>
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99 <option value="Trypsin">Trypsin</option>
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100 </param>
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101
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102 <param name="instrument" type="select" format="text">
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103 <label>Instrument Type</label>
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104 <option value="2">TOF</option>
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105 <option value="0">Low-res LCQ/LTQ</option>
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106 <option value="1">High-res LTQ</option>
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107 </param>
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108
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109 <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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110
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111 <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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112 <param name="precursor_tolu" type="select" format="text">
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113 <label>Precursor Ion Tolerance Units</label>
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114 <option value="ppm">ppm</option>
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115 <option value="Da">Da</option>
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116 </param>
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117
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118 </inputs>
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119
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120
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121 <outputs>
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122 <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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123 </outputs>
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124
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125
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126 <help>
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127
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128 **What it does**
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129
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130 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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131
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132 ----
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133
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134 **References**
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135
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136 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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137
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138 </help>
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139
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140 </tool>
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