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1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
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2
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3 <requirements>
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4
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4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
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5 <requirement type="package" version="2.1.9">omssa</requirement>
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1
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6 <requirement type="package" version="2.2.27">blast</requirement>
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7 </requirements>
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8
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9
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0
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10 <description>Run an OMSSA MS/MS Search</description>
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11
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4
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12 <command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb
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13
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14 #if $database.source_select=="built_in":
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15 -d $database.dbkey
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16 #else
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17 -d $database.fasta_file
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0
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18 #end if
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19
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20 --var-mods='
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21 $variable_mods
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22 '
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23
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24 --fix-mods='
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25 $fixed_mods
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26 '
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27
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28 --searched-ions='
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29 $searched_ions
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30 '
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31
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4
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32 $input_file
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33 -o $output
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34 -r
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35
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36 --enzyme=$enzyme
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37
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38 --precursor-ion-tol-units=$precursor_tolu
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39
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40 -v $missed_cleavages
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41
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42 -f $fragment_ion_tol
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43
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44 -p $precursor_ion_tol
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45
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46 --num-peaks-for-multi-isotope-search $multi_isotope
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47
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48 $use_average_mass
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49 $respect_precursor_charges
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50
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51 --max-hit-expect $max_hit_expect
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52
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53 --intensity-cut-off $intensity_cut_off
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0
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54
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55 </command>
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56
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57
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58 <inputs>
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59 <conditional name="database">
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60 <param name="source_select" type="select" label="Database source">
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61 <option value="built_in">Built-In</option>
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62 <option value="input_ref">Uploaded fasta file</option>
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63 </param>
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64 <when value="built_in">
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65 <param name="dbkey" type="select" format="text" >
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66 <label>Database</label>
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67 <options from_file="pepxml_databases.loc">
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68 <column name="name" index="0" />
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69 <column name="value" index="2" />
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70 </options>
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71 </param>
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72 </when>
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73 <when value="input_ref">
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74 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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75 </when>
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76 </conditional>
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77
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78 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
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79
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80 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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81 clicking to select multiple items">
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82 <options from_file="omssa_mods.loc">
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83 <column name="name" index="0" />
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84 <column name="value" index="2" />
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85 </options>
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86 </param>
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87
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88 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
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89 clicking to select multiple items">
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90 <options from_file="omssa_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
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97 <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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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="0">Trypsin</option>
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107 <option value="1">Arg-C</option>
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108 <option value="2">CNBr</option>
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109 <option value="3">Chymotrypsin (FYWL)</option>
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110 <option value="4">Formic Acid</option>
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111 <option value="5">Lys-C</option>
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112 <option value="6">Lys-C, no P rule</option>
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113 <option value="7">Pepsin A</option>
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114 <option value="8">Trypsin+CNBr</option>
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115 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
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116 <option value="10">Trypsin, no P rule</option>
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117 <option value="11">Whole protein</option>
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118 <option value="12">Asp-N</option>
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119 <option value="13">Glu-C</option>
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120 <option value="14">Asp-N+Glu-C</option>
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121 <option value="15">Top-Down</option>
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122 <option value="16">Semi-Tryptic</option>
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123 <option value="17">No Enzyme</option>
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124 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
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125 <option value="19">Asp-N (DE)</option>
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126 <option value="20">Glu-C (DE)</option>
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127 <option value="21">Lys-N (K)</option>
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128 <option value="22">Thermolysin, no P rule</option>
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129 <option value="23">Semi-Chymotrypsin (FYWL)</option>
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130 <option value="24">Semi-Glu-C</option>
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131 </param>
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132
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133 <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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134 <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
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135 <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci-->
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136
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137
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138 <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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139 <param name="precursor_tolu" type="select" format="text">
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140 <label>Precursor Ion Tolerance Units</label>
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141 <option value="ppm">ppm</option>
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142 <option value="Da">Da</option>
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143 </param>
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144
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145 <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/>
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146 <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/>
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147
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148 <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search">
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149 <label>Multi-isotope search.</label>
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150 <option value="0">0</option>
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151 <option value="1">1</option>
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152 <option value="2">2</option>
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153 <option value="3">3</option>
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154 <option value="4">4</option>
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155 </param>
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156
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157 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
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158 <option selected="true" value="0">a</option>
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159 <option selected="true" value="1">b</option>
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160 <option value="2">c</option>
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161 <option selected="true" value="3">x</option>
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162 <option selected="true" value="4">y</option>
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163 <option value="5">zdot</option>
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164 <option value="10">adot</option>
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165 <option value="11">x-CO2</option>
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166 <option value="12">adot-CO2</option>
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167 </param>
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168
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169 </inputs>
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170
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171 <outputs>
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172 <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/>
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173 </outputs>
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174
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175 <help>
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176 **What it does**
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177
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178 Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
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179
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180 ----
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181
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182 **Citation**
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183
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184 If you use this tool please read and cite the paper describing OMSSA.
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185
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186 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
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187
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188 </help>
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189 </tool>
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