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1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
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2 <description>Run an MSGF+ Search</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.1</container>
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5 <requirement type="package" version="1.4">protk</requirement>
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6 <requirement type="package" version="20140210">msgfplus</requirement>
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7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
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8 </requirements>
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9 <command>
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10 msgfplus_search.rb
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11 #if $database.source_select=="built_in":
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12 --galaxy -d $database.dbkey
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13 #else
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14 --galaxy -d $database.fasta_file
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15 #end if
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16
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17 --var-mods='
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18 $variable_mods
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19 #for $custom_variable_mod in $custom_variable_mods:
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20 ,${custom_variable_mod.custom_mod}
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21 #end for
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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 #for $custom_fix_mod in $custom_fix_mods:
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27 ,${custom_fix_mod.custom_mod}
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28 #end for
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29 '
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30
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31 $input_file
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32 -o $output
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33 -r
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34 --enzyme=$enzyme
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35 --precursor-ion-tol-units=$precursor_tolu
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36 -v $missed_cleavages
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37 $cleavage_semi
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38 -p $precursor_ion_tol
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39 --instrument=$instrument
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40 --isotope-error-range=$isotope_error_range
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41 --fragment-method=$fragment_method
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42 --protocol=$protocol
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43 --min-pep-len=$min_pep_len
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44 --max-pep-len=$max_pep_len
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45 --max-pep-charge=$max_pep_charge
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46 --min-pep-charge=$min_pep_charge
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47 --num-reported-matches=$num_reported_matches
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48 --java-mem=$java_mem
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49
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50 --threads $threads
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51
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52 #if $pepxml_output_use:
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53 --pepxml
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54 #end if
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55 </command>
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56
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57 <inputs>
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58 <conditional name="database">
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59 <param name="source_select" type="select" label="Database source">
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60 <option value="built_in">Built-In</option>
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61 <option value="input_ref" selected="true">Your Upload File</option>
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62 </param>
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63 <when value="built_in">
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64 <param name="dbkey" type="select" format="text" >
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65 <label>Database</label>
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66 <options from_file="pepxml_databases.loc">
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67 <column name="name" index="0" />
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68 <column name="value" index="2" />
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69 </options>
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70 </param>
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71 </when>
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72 <when value="input_ref">
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73 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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74 </when>
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75 </conditional>
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76 <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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77 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
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78 <options from_file="msgfplus_mods.loc">
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79 <column name="name" index="0" />
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80 <column name="value" index="2" />
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81 </options>
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82 </param>
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83 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
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84 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
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85 <param name="custom_mod" type="text" />
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86 </repeat>
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87 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
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88 <options from_file="msgfplus_mods.loc">
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89 <column name="name" index="0" />
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90 <column name="value" index="2" />
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91 </options>
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92 </param>
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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 <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 selected="true" value="2">2</option>
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102 </param>
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103
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104 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
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105
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106 <param name="enzyme" type="select" format="text">
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107 <label>Enzyme</label>
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108 <option value="0">unspecific cleavage</option>
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109 <option value="1" selected="true">Trypsin</option>
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110 <option value="2">Chymotrypsin</option>
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111 <option value="3">Lys-C</option>
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112 <option value="4">Lys-N</option>
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113 <option value="5">glutamyl endopeptidase</option>
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114 <option value="6">Arg-C</option>
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115 <option value="7">Asp-N</option>
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116 <option value="8">alphaLP</option>
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117 <option value="9">no cleavage</option>
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118 </param>
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119
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120 <param name="instrument" type="select" format="text">
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121 <label>Instrument Type</label>
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122 <option value="2">TOF</option>
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123 <option value="0" selected="true">Low-res LCQ/LTQ</option>
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124 <option value="1">High-res LTQ</option>
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125 </param>
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126
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127 <param name="fragment_method" type="select" format="text">
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128 <label>Fragmentation Method</label>
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129 <option value="0">Respect Input File</option>
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130 <option value="1">CID</option>
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131 <option value="2">ETD</option>
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132 <option value="3">HCD</option>
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133 <option value="4">Merge spectra from same precursor</option>
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134 </param>
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135
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136 <param name="protocol" type="select" format="text">
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137 <label>Protocol</label>
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138 <option value="0">NoProtocol</option>
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139 <option value="1">Phosphorylation</option>
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140 <option value="2">iTRAQ</option>
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141 <option value="3">iTRAQPhospho</option>
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142 </param>
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143
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144 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
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145 <param name="precursor_tolu" type="select" format="text">
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146 <label>Precursor Ion Tolerance Units</label>
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147 <option value="ppm">ppm</option>
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148 <option value="Da">Da</option>
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149 </param>
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150
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151 <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/>
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152 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
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153 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
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154 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
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155 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
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156 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
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157 <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
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158 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>
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159 <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
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160 </inputs>
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161 <outputs>
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162 <data format="mzid" 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' if $pepxml_output_use else 'mzid'}">
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163 <change_format>
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164 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
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165 </change_format>
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166 </data>
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167 </outputs>
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168
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169 <tests>
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170 <!-- Just test that the tool runs and produces vaguely correct output -->
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171 <test>
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172 <param name="source_select" value="input_ref"/>
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173 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
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174 <param name="input_file" value="tiny.mzML" format="mzml"/>
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175 <param name="precursor_ion_tol" value="200"/>
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176 <param name="pepxml_output_use" value="true"/>
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177 <output name="output" format="raw_pepxml">
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178 <assert_contents>
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179 <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" />
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180 </assert_contents>
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181 </output>
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182 </test>
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183 </tests>
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184
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185 <help>
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186
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187 **What it does**
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188
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189 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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190
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191 ----
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192
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193 **References**
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194
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195 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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196
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197 </help>
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198 </tool>
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