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4
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0">
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3
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2 <description>
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11
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3 Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
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3
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.28.0">peptide_shaker</requirement>
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7 <requirement type="package" version="1.18.0">searchgui</requirement>
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6
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8 <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
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9 </requirements>
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3
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Job Failed" />
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12 </stdio>
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13 <command>
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14 #from datetime import datetime
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15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 mkdir output;
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18 mkdir output_reports;
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19 cwd=`pwd`;
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20 #for $mgf in $peak_lists:
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21 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
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22 ln -s '${mgf}' '${input_name}';
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23 #end for
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24 ##ln -s "${input_database}" input_database.fasta;
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25 cp "${input_database}" input_database.fasta;
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26
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27 ###########################################
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28 #### Creating decoy database ####
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29 ###########################################
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30 #if $create_decoy:
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31 echo "Creating decoy database.";
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32 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
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33 rm input_database.fasta;
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34 cp input_database_concatenated_target_decoy.fasta input_database.fasta;
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35 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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36 #end if
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37
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38 #####################################################
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39 ## generate IdentificationParameters for SearchGUI ##
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40 #####################################################
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41
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42 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
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43 -out SEARCHGUI_IdentificationParameters.parameters
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2
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44 -prec_ppm "${precursor_ion_tol_units}"
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45 -prec_tol "${precursor_ion_tol}"
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46 -frag_tol "${fragment_tol}"
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47 -enzyme "${enzyme}"
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48 #set $fixed_mods_str = $fixed_modifications or ''
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49 #set $variable_mods_str = $variable_modifications or ''
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50 #if $fixed_mods_str
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51 -fixed_mods "${fixed_mods_str}"
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52 #end if
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53 #if $variable_mods_str
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54 -variable_mods "${variable_mods_str}"
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55 #end if
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56 -min_charge "${min_charge}"
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57 -max_charge "${max_charge}"
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58 -mc "${missed_cleavages}"
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59 -fi "${forward_ion}"
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60 -ri "${reverse_ion}"
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1
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61 -db input_database.fasta
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62
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63 #if $advanced.advanced_type_selector == "advanced":
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64
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65 ##if $advanced.xtandem.xtandem_selector == "yes"
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66 ##end if
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67
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68 #if $advanced.omssa.omssa_selector == "yes"
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69 -omssa_hitlist_length ${advanced.omssa.hitlist_length}
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70 -omssa_remove_prec ${advanced.omssa.remove_precursor}
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71 -omssa_scale_prec ${advanced.omssa.scale_precursor}
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72 -omssa_estimate_charge ${advanced.omssa.estimate_charge}
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73 #end if
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74
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75 ##if $advanced.msgf.msgf_selector == "yes"
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76 ##end if
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77
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78 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
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79 ##end if
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80
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81 #end if
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82 ;
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83
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84 ################
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85 ## Search CLI ##
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86 ################
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87 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
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88 -temp_folder `pwd`
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89 -spectrum_files \$cwd
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90 -output_folder \$cwd/output
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91 -id_params SEARCHGUI_IdentificationParameters.parameters
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92
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93 -threads "\${GALAXY_SLOTS:-12}"
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94 -correct_titles "${correct_titles}"
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95 -mgf_splitting "${mgf_splitting}"
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96 -mgf_spectrum_count "${mgf_spectrum_count}"
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97
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98 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
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99 ## the tree is generated afterwards in PeptideShaker
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100 -protein_tree 0
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101
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6
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102 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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103
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104 #if $advanced.advanced_type_selector == "advanced":
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105
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106 #if $advanced.xtandem.xtandem_selector == "yes"
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107 -xtandem 1
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0
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108 #else
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1
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109 -xtandem 0
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0
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110 #end if
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111
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1
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112 #if $advanced.omssa.omssa_selector == "yes"
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113 -omssa 1
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114 #else
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115 -omssa 0
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116 #end if
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117
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118 #if $advanced.msgf.msgf_selector == "yes"
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119 -msgf 1
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120 #else
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121 -msgf 0
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122 #end if
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123
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124 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
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125 -ms_amanda 1
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126 #else
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127 -ms_amanda 0
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0
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128 #end if
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1
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129
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130 #end if
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1
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131 ;
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132
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1
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133 #########################################################
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134 ## generate IdentificationParameters for PeptideShaker ##
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135 #########################################################
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136 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
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137 -out PEPTIDESHAKER_IdentificationParameters.parameters
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138 -prec_ppm "${precursor_ion_tol_units}"
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139 -prec_tol "${precursor_ion_tol}"
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140 -frag_tol "${fragment_tol}"
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141 -enzyme "${enzyme}"
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1
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142 #set $fixed_mods_str = $fixed_modifications or ''
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143 #set $variable_mods_str = $variable_modifications or ''
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144 #if $fixed_mods_str
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145 -fixed_mods "$fixed_mods_str"
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146 #end if
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147 #if $variable_mods_str
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148 -variable_mods "$variable_mods_str"
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149 #end if
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150 -min_charge $min_charge
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151 -max_charge $max_charge
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152 -mc $missed_cleavages
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153 -fi $forward_ion
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154 -ri $reverse_ion
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155 -db input_database.fasta
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156 ;
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157
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1
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158 ######################
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159 ## PeptideShakerCLI ##
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160 ######################
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161 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
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162 -temp_folder `pwd`
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163 -experiment '${exp_str}'
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164 -sample '${samp_str}'
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165 -replicate 1
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166 -spectrum_files \$cwd
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167 -identification_files \$cwd/output
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168 -out \$cwd/peptide_shaker_output.cps
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169 -id_params PEPTIDESHAKER_IdentificationParameters.parameters
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170
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171 ##Optional gene annotation parameter
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172 #if $species_type.species_type_selector != 'no_species_type':
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173 -species_type "${species_type.species_type_selector}"
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174 -species "${species_type.species}"
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1
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175 #end if
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176
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177 ##Optional processing parameters:
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178 #if $processing_options.processing_options_selector == "yes"
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179 -protein_FDR "${processing_options.protein_fdr}"
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180 -peptide_FDR "${processing_options.peptide_fdr}"
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181 -psm_FDR "${processing_options.psm_fdr}"
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182 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
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183 #if $processing_options.ptm_score.ptm_score_selector == 1
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184 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
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185 #if str($processing_options.ptm_score.ptm_threshold) != ''
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186 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
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187 #end if
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188 #end if
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189 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
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190 #end if
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191
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192 ##Optional filtering parameters:
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193 #if $filtering_options.filtering_options_selector == "yes":
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194 -min_peptide_length "${filtering_options.min_peptide_length}"
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195 -max_peptide_length "${filtering_options.max_peptide_length}"
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196 -max_precursor_error "${filtering_options.max_precursor_error}"
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197 -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
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198 -max_xtandem_e "${filtering_options.max_xtandem_e}"
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199 -max_omssa_e "${filtering_options.max_omssa_e}"
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200 -max_mascot_e "${filtering_options.max_mascot_e}"
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201 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
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202 #end if
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2
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203 ;
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204
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2
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205 ##################################
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206 ## PeptideShaker Report options ##
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207 ##################################
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208 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
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209 -temp_folder `pwd`
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210 -in \$cwd/peptide_shaker_output.cps
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211 -out_reports \$cwd/output_reports
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212 #if 'cps' in str($outputs).split(','):
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213 #set $cleaned_list = str($outputs).split(',')
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214 #silent $cleaned_list.remove('cps')
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215 -reports #echo ','.join($cleaned_list)#
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216 #else:
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217 -reports #echo str($outputs)#
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218 #end if
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219 ;
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220
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221 #if '0' in str($outputs).split(','):
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222 find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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223 ;
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224 #end if
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225 #if '2' in str($outputs).split(','):
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226 find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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227 ;
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228 #end if
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229 #if '3' in str($outputs).split(','):
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230 find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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231 ;
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232 #end if
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233 #if '4' in str($outputs).split(','):
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234 find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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235 ;
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3
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236 #end if
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237 #if '1' in str($outputs).split(','):
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238 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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239 ;
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3
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240 #end if
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241
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242 ## the following line is needed. Otherwise, Galaxy will strip away the ';'
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243 echo 'Finished!';
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244 </command>
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245 <inputs>
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246 <param format="fasta" name="input_database" type="data" label="Protein Database"
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247 help="Select FASTA database from history"/>
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248
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249 <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" />
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250
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251 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
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252 help="Select appropriate MGF dataset(s) from history" />
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253 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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254 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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255 <option value="1">Parts per million (ppm)</option>
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256 <option value="0">Daltons</option>
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257 </param>
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258 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
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259 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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260 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
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261 help="Provide error value for fragment ions, based on instrument used"/>
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262 <param name="enzyme" type="select" label="Enzyme"
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263 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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264 <option value="Trypsin">Trypsin</option>
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265 <option value="Arg-C">Arg-C</option>
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266 <option value="CNBr">CNBr</option>
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267 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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268 <option value="Formic Acid">Formic Acid</option>
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269 <option value="Lys-C">Lys-C</option>
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270 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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271 <option value="Pepsin A">Pepsin A</option>
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272 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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273 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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274 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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275 <option value="whole protein">whole protein</option>
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276 <option value="Asp-N">Asp-N</option>
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277 <option value="Glu-C">Glu-C</option>
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278 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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279 <option value="Top-Down">Top-Down</option>
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280 <option value="Semi-Tryptic">Semi-Tryptic</option>
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281 <option value="No enzyme">No enzyme</option>
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282 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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283 <option value="Asp-N (DE)">Asp-N (DE)</option>
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284 <option value="Glu-C (DE)">Glu-C (DE)</option>
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285 <option value="Lys-N (K)">Lys-N (K)</option>
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286 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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287 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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1
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288 <option value="Semi-Glu-C">Semi-Glu-C</option>
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289 </param>
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290
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11
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291 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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292 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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293 <option value="0">no correction</option>
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294 <option value="1" selected="True">rename spectra</option>
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295 <option value="2">delete spectra</option>
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0
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296 </param>
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1
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297
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298 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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299 help="Choose a smaller value if you are running on a machine with limited memory"/>
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1
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300 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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11
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301 help="Choose a smaller value if you are running on a machine with limited memory"/>
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1
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302
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303 <conditional name="species_type">
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304 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
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11
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305 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
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1
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306 <option value="Fungi">Fungi</option>
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307 <option value="Plants">Plants</option>
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308 <option value="Metazoa">Metazoa</option>
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309 <option value="Vertebrates">Vertebrates</option>
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310 <option value="Protists">Protists</option>
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311 <option value="no_species_type" selected="true">No species restriction</option>
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312 </param>
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313 <when value="Protists">
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314 <param name="species" type="select" label="The species to use for the gene annotation"
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11
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315 help="">
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1
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316 <option value="Albugo laibachii">Albugo laibachii</option>
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317 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
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318 <option value="Entamoeba histolytica">Entamoeba histolytica</option>
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319 <option value="Giardia lamblia">Giardia lamblia</option>
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320 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
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321 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
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322 <option value="Leishmania major">Leishmania major</option>
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323 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
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324 <option value="Phytophthora infestans">Phytophthora infestans</option>
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325 <option value="Phytophthora ramorum">Phytophthora ramorum</option>
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326 <option value="Phytophthora sojae">Phytophthora sojae</option>
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327 <option value="Plasmodium berghei">Plasmodium berghei</option>
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328 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
|
|
|
329 <option value="Plasmodium falciparum">Plasmodium falciparum</option>
|
|
|
330 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
|
|
|
331 <option value="Plasmodium vivax">Plasmodium vivax</option>
|
|
|
332 <option value="Pythium ultimum">Pythium ultimum</option>
|
|
|
333 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
|
|
|
334 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
|
|
|
335 <option value="Toxoplasma gondii">Toxoplasma gondii</option>
|
|
|
336 <option value="Trypanosoma brucei">Trypanosoma brucei</option>
|
|
|
337 </param>
|
|
|
338 </when>
|
|
|
339 <when value="Plants">
|
|
|
340 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
11
|
341 help="">
|
|
1
|
342 <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
|
|
|
343 <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
|
|
|
344 <option value="Brachypodium distachyon">Brachypodium distachyon</option>
|
|
|
345 <option value="Brassica rapa genes">Brassica rapa genes</option>
|
|
|
346 <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>
|
|
|
347 <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option>
|
|
|
348 <option value="Glycine max">Glycine max</option>
|
|
|
349 <option value="Hordeum vulgare">Hordeum vulgare</option>
|
|
|
350 <option value="Medicago truncatula">Medicago truncatula</option>
|
|
|
351 <option value="Musa acuminata">Musa acuminata</option>
|
|
|
352 <option value="Oryza brachyantha">Oryza brachyantha</option>
|
|
|
353 <option value="Oryza glaberrima">Oryza glaberrima</option>
|
|
|
354 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
|
|
|
355 <option value="Oryza sativa">Oryza sativa</option>
|
|
|
356 <option value="Physcomitrella patens">Physcomitrella patens</option>
|
|
|
357 <option value="Populus trichocarpa">Populus trichocarpa</option>
|
|
|
358 <option value="Selaginella moellendorffii">Selaginella moellendorffii</option>
|
|
|
359 <option value="Setaria italica">Setaria italica</option>
|
|
|
360 <option value="Solanum lycopersicum">Solanum lycopersicum</option>
|
|
|
361 <option value="Solanum tuberosum">Solanum tuberosum</option>
|
|
|
362 <option value="Sorghum bicolor">Sorghum bicolor</option>
|
|
|
363 <option value="Vitis vinifera">Vitis vinifera</option>
|
|
|
364 <option value="Zea mays">Zea mays</option>
|
|
|
365 </param>
|
|
|
366 </when>
|
|
|
367 <when value="Metazoa">
|
|
|
368 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
11
|
369 help="">
|
|
1
|
370 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
|
|
|
371 <option value="Aedes aegypti">Aedes aegypti</option>
|
|
|
372 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
|
|
|
373 <option value="Anopheles darlingi">Anopheles darlingi</option>
|
|
|
374 <option value="Anopheles gambiae">Anopheles gambiae</option>
|
|
|
375 <option value="Apis mellifera">Apis mellifera</option>
|
|
|
376 <option value="Atta cephalotes">Atta cephalotes</option>
|
|
|
377 <option value="Bombyx mori">Bombyx mori</option>
|
|
|
378 <option value="Brugia malayi">Brugia malayi</option>
|
|
|
379 <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option>
|
|
|
380 <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option>
|
|
|
381 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
|
|
|
382 <option value="Caenorhabditis japonica">Caenorhabditis japonica</option>
|
|
|
383 <option value="Caenorhabditis remanei">Caenorhabditis remanei</option>
|
|
|
384 <option value="Culex quinquefasciatus">Culex quinquefasciatus</option>
|
|
|
385 <option value="Danaus plexippus">Danaus plexippus</option>
|
|
|
386 <option value="Daphnia pulex">Daphnia pulex</option>
|
|
|
387 <option value="Drosophila ananassae">Drosophila ananassae</option>
|
|
|
388 <option value="Drosophila erecta">Drosophila erecta</option>
|
|
|
389 <option value="Drosophila grimshawi">Drosophila grimshawi</option>
|
|
|
390 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
|
|
|
391 <option value="Drosophila mojavensis">Drosophila mojavensis</option>
|
|
|
392 <option value="Drosophila persimilis">Drosophila persimilis</option>
|
|
|
393 <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option>
|
|
|
394 <option value="Drosophila sechellia">Drosophila sechellia</option>
|
|
|
395 <option value="Drosophila simulans">Drosophila simulans</option>
|
|
|
396 <option value="Drosophila virilis">Drosophila virilis</option>
|
|
|
397 <option value="Drosophila willistoni">Drosophila willistoni</option>
|
|
|
398 <option value="Drosophila yakuba">Drosophila yakuba</option>
|
|
|
399 <option value="Heliconius melpomene">Heliconius melpomene</option>
|
|
|
400 <option value="Ixodes scapularis">Ixodes scapularis</option>
|
|
|
401 <option value="Loa loa">Loa loa</option>
|
|
|
402 <option value="Megaselia scalaris">Megaselia scalaris</option>
|
|
|
403 <option value="Nasonia vitripennis">Nasonia vitripennis</option>
|
|
|
404 <option value="Nematostella vectensis">Nematostella vectensis</option>
|
|
|
405 <option value="Pediculus humanus">Pediculus humanus</option>
|
|
|
406 <option value="Pristionchus pacificus">Pristionchus pacificus</option>
|
|
|
407 <option value="Schistosoma mansoni">Schistosoma mansoni</option>
|
|
|
408 <option value="Strigamia maritima">Strigamia maritima</option>
|
|
|
409 <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option>
|
|
|
410 <option value="Tribolium castaneum">Tribolium castaneum</option>
|
|
|
411 <option value="Trichinella spiralis">Trichinella spiralis</option>
|
|
|
412 <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
|
|
|
413 </param>
|
|
|
414 </when>
|
|
|
415 <when value="Fungi">
|
|
|
416 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
11
|
417 help="">
|
|
1
|
418 <option value="Ashbya gossypii">Ashbya gossypii</option>
|
|
|
419 <option value="Aspergillus clavatus">Aspergillus clavatus</option>
|
|
|
420 <option value="Aspergillus flavus">Aspergillus flavus</option>
|
|
|
421 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
|
|
|
422 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
|
|
|
423 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
|
|
|
424 <option value="Aspergillus niger">Aspergillus niger</option>
|
|
|
425 <option value="Aspergillus oryzae">Aspergillus oryzae</option>
|
|
|
426 <option value="Aspergillus terreus">Aspergillus terreus</option>
|
|
|
427 <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option>
|
|
|
428 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
|
|
|
429 <option value="Fusarium oxysporum">Fusarium oxysporum</option>
|
|
|
430 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
|
|
|
431 <option value="Gibberella moniliformis">Gibberella moniliformis</option>
|
|
|
432 <option value="Gibberella zeae">Gibberella zeae</option>
|
|
|
433 <option value="Glomerella graminicola">Glomerella graminicola</option>
|
|
|
434 <option value="Komagataella pastoris">Komagataella pastoris</option>
|
|
|
435 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
|
|
|
436 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
|
|
|
437 <option value="Magnaporthe poae">Magnaporthe poae</option>
|
|
|
438 <option value="Melampsora larici-populina">Melampsora larici-populina</option>
|
|
|
439 <option value="Nectria haematococca">Nectria haematococca</option>
|
|
|
440 <option value="Neosartorya fischeri">Neosartorya fischeri</option>
|
|
|
441 <option value="Neurospora crassa">Neurospora crassa</option>
|
|
|
442 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
|
|
|
443 <option value="Puccinia graminis">Puccinia graminis</option>
|
|
|
444 <option value="Puccinia triticina">Puccinia triticina</option>
|
|
|
445 <option value="Pyrenophora teres">Pyrenophora teres</option>
|
|
|
446 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
|
|
|
447 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
|
|
|
448 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
|
|
|
449 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
|
|
|
450 <option value="Sporisorium reilianum">Sporisorium reilianum</option>
|
|
|
451 <option value="Trichoderma reesei">Trichoderma reesei</option>
|
|
|
452 <option value="Trichoderma virens">Trichoderma virens</option>
|
|
|
453 <option value="Tuber melanosporum">Tuber melanosporum</option>
|
|
|
454 <option value="Ustilago maydis">Ustilago maydis</option>
|
|
|
455 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
|
|
|
456 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
|
|
|
457 </param>
|
|
|
458 </when>
|
|
|
459 <when value="Vertebrates">
|
|
|
460 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
11
|
461 help="">
|
|
1
|
462 <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
|
|
|
463 <option value="Anolis carolinensis">Anolis carolinensis</option>
|
|
|
464 <option value="Bos taurus">Bos taurus</option>
|
|
|
465 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
|
|
|
466 <option value="Callithrix jacchus">Callithrix jacchus</option>
|
|
|
467 <option value="Canis familiaris">Canis familiaris</option>
|
|
|
468 <option value="Cavia porcellus">Cavia porcellus</option>
|
|
|
469 <option value="Choloepus hoffmanni">Choloepus hoffmanni</option>
|
|
|
470 <option value="Ciona intestinalis">Ciona intestinalis</option>
|
|
|
471 <option value="Ciona savignyi">Ciona savignyi</option>
|
|
|
472 <option value="Danio rerio">Danio rerio</option>
|
|
|
473 <option value="Dasypus novemcinctus">Dasypus novemcinctus</option>
|
|
|
474 <option value="Dipodomys ordii">Dipodomys ordii</option>
|
|
|
475 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
|
|
|
476 <option value="Echinops telfairi">Echinops telfairi</option>
|
|
|
477 <option value="Equus caballus">Equus caballus</option>
|
|
|
478 <option value="Erinaceus europaeus">Erinaceus europaeus</option>
|
|
|
479 <option value="Felis catus">Felis catus</option>
|
|
|
480 <option value="Gallus gallus">Gallus gallus</option>
|
|
|
481 <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option>
|
|
|
482 <option value="Gorilla gorilla">Gorilla gorilla</option>
|
|
|
483 <option value="Homo sapiens">Homo sapiens</option>
|
|
|
484 <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option>
|
|
|
485 <option value="Latimeria chalumnae">Latimeria chalumnae</option>
|
|
|
486 <option value="Loxodonta africana">Loxodonta africana</option>
|
|
|
487 <option value="Macaca mulatta">Macaca mulatta</option>
|
|
|
488 <option value="Macropus eugenii">Macropus eugenii</option>
|
|
|
489 <option value="Meleagris gallopavo">Meleagris gallopavo</option>
|
|
|
490 <option value="Microcebus murinus">Microcebus murinus</option>
|
|
|
491 <option value="Monodelphis domestica">Monodelphis domestica</option>
|
|
|
492 <option value="Mus musculus">Mus musculus</option>
|
|
|
493 <option value="Mustela putorius furo">Mustela putorius furo</option>
|
|
|
494 <option value="Myotis lucifugus">Myotis lucifugus</option>
|
|
|
495 <option value="Nomascus leucogenys">Nomascus leucogenys</option>
|
|
|
496 <option value="Ochotona princeps">Ochotona princeps</option>
|
|
|
497 <option value="Oreochromis niloticus">Oreochromis niloticus</option>
|
|
|
498 <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
|
|
|
499 <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
|
|
|
500 <option value="Oryzias latipes">Oryzias latipes</option>
|
|
|
501 <option value="Otolemur garnettii">Otolemur garnettii</option>
|
|
|
502 <option value="Pan troglodytes">Pan troglodytes</option>
|
|
|
503 <option value="Petromyzon marinus">Petromyzon marinus</option>
|
|
|
504 <option value="Pelodiscus sinensis">Pelodiscus sinensis</option>
|
|
|
505 <option value="Pongo abelii">Pongo abelii</option>
|
|
|
506 <option value="Procavia capensis">Procavia capensis</option>
|
|
|
507 <option value="Pteropus vampyrus">Pteropus vampyrus</option>
|
|
|
508 <option value="Rattus norvegicus">Rattus norvegicus</option>
|
|
|
509 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
|
|
|
510 <option value="Sarcophilus harrisii">Sarcophilus harrisii</option>
|
|
|
511 <option value="Sorex araneus">Sorex araneus</option>
|
|
|
512 <option value="Sus scrofa">Sus scrofa</option>
|
|
|
513 <option value="Taeniopygia guttata">Taeniopygia guttata</option>
|
|
|
514 <option value="Takifugu rubripes">Takifugu rubripes</option>
|
|
|
515 <option value="Tarsius syrichta">Tarsius syrichta</option>
|
|
|
516 <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option>
|
|
|
517 <option value="Tupaia belangeri">Tupaia belangeri</option>
|
|
|
518 <option value="Tursiops truncatus">Tursiops truncatus</option>
|
|
|
519 <option value="Vicugna pacos">Vicugna pacos</option>
|
|
|
520 <option value="Xenopus tropicalis">Xenopus tropicalis</option>
|
|
|
521 <option value="Xiphophorus maculatus">Xiphophorus maculatus</option>
|
|
|
522 </param>
|
|
|
523 </when>
|
|
|
524 </conditional>
|
|
|
525
|
|
0
|
526 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
|
|
11
|
527 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
|
|
0
|
528 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
|
|
|
529 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
|
|
|
530 <options from_file="searchgui_mods.loc">
|
|
|
531 <column name="name" index="0" />
|
|
|
532 <column name="value" index="0" />
|
|
|
533 </options>
|
|
|
534 </param>
|
|
|
535 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
|
|
|
536 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
|
|
|
537 <options from_file="searchgui_mods.loc">
|
|
|
538 <column name="name" index="0" />
|
|
|
539 <column name="value" index="0" />
|
|
|
540 </options>
|
|
|
541 </param>
|
|
|
542 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
|
|
|
543 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
|
|
|
544 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
|
|
|
545 <option value="a">a</option>
|
|
|
546 <option value="b" selected="true">b</option>
|
|
|
547 <option value="c">c</option>
|
|
|
548 </param>
|
|
|
549 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
|
|
|
550 <option value="x">x</option>
|
|
|
551 <option value="y" selected="true">y</option>
|
|
|
552 <option value="z">z</option>
|
|
|
553 </param>
|
|
|
554 <conditional name="advanced">
|
|
1
|
555 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
|
|
|
556 <option value="basic" selected="True">Basic</option>
|
|
|
557 <option value="advanced">Advanced</option>
|
|
|
558 </param>
|
|
|
559 <when value="basic" />
|
|
|
560 <when value="advanced">
|
|
0
|
561 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
|
|
1
|
562
|
|
|
563 <conditional name="xtandem">
|
|
|
564 <param name="xtandem_selector" type="select" label="Run X!Tandem search">
|
|
|
565 <option value="yes" selected="True">Search with X!Tandem</option>
|
|
|
566 <option value="no">No X!Tandem search</option>
|
|
|
567 </param>
|
|
|
568 <when value="no" />
|
|
|
569 <when value="yes">
|
|
|
570 </when>
|
|
|
571 </conditional>
|
|
|
572
|
|
0
|
573 <conditional name="omssa">
|
|
1
|
574 <param name="omssa_selector" type="select" label="Run OMSSA search">
|
|
|
575 <option value="yes" selected="True">Search with OMSSA</option>
|
|
|
576 <option value="no">No OMSSA search</option>
|
|
|
577 </param>
|
|
|
578 <when value="no" />
|
|
|
579 <when value="yes">
|
|
0
|
580 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
|
|
|
581 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
|
|
|
582 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
|
|
|
583 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
|
|
|
584 </when>
|
|
|
585 </conditional>
|
|
1
|
586
|
|
|
587 <conditional name="msgf">
|
|
|
588 <param name="msgf_selector" type="select" label="Run MSGF search">
|
|
|
589 <option value="yes" selected="True">Search with MSGF</option>
|
|
|
590 <option value="no">No MSGF search</option>
|
|
|
591 </param>
|
|
|
592 <when value="no" />
|
|
|
593 <when value="yes">
|
|
|
594 </when>
|
|
|
595 </conditional>
|
|
|
596
|
|
|
597 <conditional name="ms_amanda">
|
|
|
598 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
|
|
7
|
599 <option value="yes">Search with MS Amanda</option>
|
|
|
600 <option value="no" selected="True">No MS Amanda search</option>
|
|
1
|
601 </param>
|
|
|
602 <when value="no" />
|
|
|
603 <when value="yes">
|
|
|
604 </when>
|
|
|
605 </conditional>
|
|
0
|
606 </when>
|
|
|
607 </conditional>
|
|
|
608 <conditional name="processing_options">
|
|
1
|
609 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
|
|
|
610 <option value="no" selected="True">Default Processing Options</option>
|
|
|
611 <option value="yes">Advanced Processing Options</option>
|
|
|
612 </param>
|
|
|
613 <when value="no" />
|
|
|
614 <when value="yes">
|
|
0
|
615 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
|
616 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
|
617 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
1
|
618 <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
|
|
11
|
619 help="default 95%: '95.0'" />
|
|
1
|
620 <conditional name="ptm_score">
|
|
|
621 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
|
|
|
622 <option value="0" selected="True">A-score</option>
|
|
|
623 <option value="1">PhosphoRS</option>
|
|
|
624 </param>
|
|
0
|
625 <when value="0" />
|
|
|
626 <when value="1">
|
|
1
|
627 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
|
|
|
628 <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
|
|
11
|
629 help="Automatic mode will be used if not set" />
|
|
0
|
630 </when>
|
|
|
631 </conditional>
|
|
|
632 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
|
|
|
633 </when>
|
|
|
634 </conditional>
|
|
|
635 <conditional name="filtering_options">
|
|
1
|
636 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
|
|
|
637 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
|
|
|
638 <option value="no" selected="True">Default Filtering Options</option>
|
|
|
639 <option value="yes">Advanced Processing Options</option>
|
|
|
640 </param>
|
|
|
641 <when value="no" />
|
|
|
642 <when value="yes">
|
|
0
|
643 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
|
|
|
644 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
|
|
11
|
645 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" />
|
|
0
|
646 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
|
|
|
647 <option value="0">ppm</option>
|
|
|
648 <option value="1">Daltons</option>
|
|
|
649 </param>
|
|
1
|
650 <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
|
|
|
651 <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
|
|
11
|
652 <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" />
|
|
0
|
653 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
|
|
|
654 </when>
|
|
|
655 </conditional>
|
|
3
|
656
|
|
|
657 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
|
|
4
|
658 <option value="3" selected="True">Peptide Report</option>
|
|
|
659 <option value="4" selected="True">Protein Report</option>
|
|
|
660 <option value="2">PSM Report</option>
|
|
3
|
661 <option value="0">Certificate of Analysis</option>
|
|
4
|
662 <option value="1">Hierarchical Report</option>
|
|
3
|
663 <option value="cps">CPS file</option>
|
|
11
|
664 <validator type="no_options" message="Please select at least one output file" />
|
|
3
|
665 </param>
|
|
0
|
666 </inputs>
|
|
|
667 <outputs>
|
|
3
|
668 <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
|
|
|
669 <filter>'cps' in outputs</filter>
|
|
|
670 </data>
|
|
5
|
671 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
|
|
3
|
672 <filter>'0' in outputs</filter>
|
|
|
673 </data>
|
|
5
|
674 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
|
|
3
|
675 <filter>'2' in outputs</filter>
|
|
|
676 </data>
|
|
4
|
677 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
|
|
3
|
678 <filter>'3' in outputs</filter>
|
|
|
679 </data>
|
|
4
|
680 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
|
|
3
|
681 <filter>'4' in outputs</filter>
|
|
|
682 </data>
|
|
4
|
683 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
|
|
|
684 <filter>'1' in outputs</filter>
|
|
|
685 </data>
|
|
0
|
686 </outputs>
|
|
7
|
687 <tests>
|
|
|
688 <test>
|
|
|
689 <param name="input_database" value="tinydb.fasta"/>
|
|
|
690 <param name="peak_lists" value="tinyspectra.mgf"/>
|
|
|
691 <param name="precursor_ion_tol" value="100"/>
|
|
|
692 <param name="fixed_modifications" value="carbamidomethyl c"/>
|
|
|
693 <param name="variable_modifications" value="oxidation of m"/>
|
|
|
694 <param name="min_charge" value="1"/>
|
|
|
695 <param name="max_charge" value="3"/>
|
|
|
696 <param name="advanced_type_selector" value="advanced"/>
|
|
|
697 <param name="xtandem_selector" value="yes"/>
|
|
|
698 <param name="omssa_selector" value="no"/>
|
|
|
699 <param name="msgf_selector" value="yes"/>
|
|
|
700 <param name="ms_amanda_selector" value="no"/>
|
|
|
701
|
|
|
702 <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" />
|
|
|
703 </test>
|
|
|
704 </tests>
|
|
0
|
705 <help>
|
|
|
706 **What it does**
|
|
|
707
|
|
|
708 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
|
|
|
709
|
|
4
|
710 https://code.google.com/p/peptide-shaker/
|
|
11
|
711
|
|
4
|
712 https://code.google.com/p/searchgui/
|
|
|
713
|
|
11
|
714 ----
|
|
4
|
715
|
|
11
|
716 Reports
|
|
|
717 =======
|
|
4
|
718
|
|
|
719
|
|
11
|
720 PSM Report
|
|
|
721 ----------
|
|
4
|
722
|
|
11
|
723 * Protein(s): Protein(s) to which the peptide can be attached
|
|
|
724 * Sequence: Sequence of the peptide
|
|
|
725 * Variable Modifications: The variable modifications
|
|
|
726 * D-score: D-score for variable PTM localization
|
|
|
727 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
|
|
|
728 * Localization Confidence: The confidence in variable PTM localization.
|
|
|
729 * Fixed Modifications: The fixed modifications.
|
|
|
730 * Spectrum File: The spectrum file.
|
|
|
731 * Spectrum Title: The title of the spectrum.
|
|
|
732 * Spectrum Scan Number: The spectrum scan number.
|
|
|
733 * RT: Retention time
|
|
|
734 * m/z: Measured m/z
|
|
|
735 * Measured Charge: The charge as given in the spectrum file.
|
|
|
736 * Identification Charge: The charge as inferred by the search engine.
|
|
|
737 * Theoretical Mass: The theoretical mass of the peptide.
|
|
|
738 * Isotope Number: The isotope number targetted by the instrument.
|
|
|
739 * Precursor m/z Error: The precursor m/z matching error.
|
|
|
740 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
|
|
|
741 * Confidence: Confidence in percent associated to the retained PSM.
|
|
|
742 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
743 * Validation: Indicates the validation level of the protein group.
|
|
4
|
744
|
|
|
745
|
|
11
|
746 Protein Report
|
|
|
747 --------------
|
|
|
748
|
|
|
749 * Main Accession: Main accession of the protein group.
|
|
|
750 * Description: Description of the protein designed by the main accession.
|
|
|
751 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
|
|
|
752 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
|
|
|
753 * PI: Protein Inference status of the protein group.
|
|
|
754 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
|
|
|
755 * Protein Group: The complete protein group (alphabetical order).
|
|
|
756 * #Peptides: Total number of peptides.
|
|
|
757 * #Validated Peptides: Number of validated peptides.
|
|
|
758 * #Unique: Total number of peptides unique to this protein group.
|
|
|
759 * #PSMs: Number of PSMs
|
|
|
760 * #Validated PSMs: Number of validated PSMs
|
|
|
761 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
|
|
|
762 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
|
|
|
763 * MW (kDa): Molecular Weight.
|
|
|
764 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
|
|
|
765 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
|
|
|
766 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
|
|
|
767 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
|
|
|
768 * Score: Score of the protein group.
|
|
|
769 * Confidence: Confidence in percent associated to the protein group.
|
|
|
770 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
|
|
|
771 * Validation: Indicates the validation level of the protein group.
|
|
|
772
|
|
|
773
|
|
|
774 Peptide Report
|
|
|
775 --------------
|
|
4
|
776
|
|
|
777
|
|
11
|
778 * Protein(s): Protein(s) to which this peptide can be attached.
|
|
|
779 * AAs Before: The amino-acids before the sequence.
|
|
|
780 * Sequence: Sequence of the peptide.
|
|
|
781 * AAs After: The amino-acids after the sequence.
|
|
|
782 * Modified Sequence: The peptide sequence annotated with variable modifications.
|
|
|
783 * Variable Modifications: The variable modifications.
|
|
|
784 * Localization Confidence: The confidence in PTMs localization.
|
|
|
785 * Fixed Modifications: The fixed modifications.
|
|
|
786 * #Validated PSMs: Number of validated PSMs.
|
|
|
787 * #PSMs: Number of PSMs.
|
|
|
788 * Score: Score of the peptide.
|
|
|
789 * Confidence: Confidence in percent associated to the peptide.
|
|
|
790 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
791 * Validation: Indicates the validation level of the protein group.
|
|
4
|
792
|
|
|
793
|
|
11
|
794 Hierachical Report
|
|
|
795 ------------------
|
|
4
|
796
|
|
11
|
797 * Main Accession: Main accession of the protein group.
|
|
|
798 * Description: Description of the protein designed by the main accession.
|
|
|
799 * PI: Protein Inference status of the protein group.
|
|
|
800 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
|
|
|
801 * Protein Group: The complete protein group (alphabetical order).
|
|
|
802 * #Peptides: Total number of peptides.
|
|
|
803 * #Validated Peptides: Number of validated peptides.
|
|
|
804 * #Unique: Total number of peptides unique to this protein group.
|
|
|
805 * #PSMs: Number of PSMs
|
|
|
806 * #Validated PSMs: Number of validated PSMs
|
|
|
807 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
|
|
|
808 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
|
|
|
809 * MW (kDa): Molecular Weight.
|
|
|
810 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
|
|
|
811 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
|
|
|
812 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
|
|
|
813 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
|
|
|
814 * Score: Score of the protein group.
|
|
|
815 * Confidence: Confidence in percent associated to the protein group.
|
|
|
816 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
|
|
|
817 * Validation: Indicates the validation level of the protein group.
|
|
|
818 * Protein(s): Protein(s) to which this peptide can be attached.
|
|
|
819 * AAs Before: The amino-acids before the sequence.
|
|
|
820 * Sequence: Sequence of the peptide.
|
|
|
821 * AAs After: The amino-acids after the sequence.
|
|
|
822 * Variable Modifications: The variable modifications.
|
|
|
823 * Localization Confidence: The confidence in PTMs localization.
|
|
|
824 * Fixed Modifications: The fixed modifications.
|
|
|
825 * #Validated PSMs: Number of validated PSMs.
|
|
|
826 * #PSMs: Number of PSMs.
|
|
|
827 * Score: Score of the peptide.
|
|
|
828 * Confidence: Confidence in percent associated to the peptide.
|
|
|
829 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
830 * Validation: Indicates the validation level of the protein group.
|
|
|
831 * Protein(s): Protein(s) to which the peptide can be attached.
|
|
|
832 * Sequence: Sequence of the peptide.
|
|
|
833 * Modified Sequence: The peptide sequence annotated with variable modifications.
|
|
|
834 * Variable Modifications: The variable modifications.
|
|
|
835 * D-score: D-score for variable PTM localization.
|
|
|
836 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
|
|
|
837 * Localization Confidence: The confidence in variable PTM localization.
|
|
|
838 * Fixed Modifications: The fixed modifications.
|
|
|
839 * Spectrum File: The spectrum file.
|
|
|
840 * Spectrum Title: The title of the spectrum.
|
|
|
841 * Spectrum Scan Number: The spectrum scan number.
|
|
|
842 * RT: Retention time
|
|
|
843 * m/z: Measured m/z
|
|
|
844 * Measured Charge: The charge as given in the spectrum file.
|
|
|
845 * Identification Charge: The charge as inferred by the search engine.
|
|
|
846 * Theoretical Mass: The theoretical mass of the peptide.
|
|
|
847 * Isotope Number: The isotope number targetted by the instrument.
|
|
|
848 * Precursor m/z Error: The precursor m/z matching error.
|
|
|
849 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
|
|
|
850 * Confidence: Confidence in percent associated to the retained PSM.
|
|
|
851 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
852 * Validation: Indicates the validation level of the protein group.
|
|
4
|
853
|
|
|
854
|
|
|
855
|
|
|
856
|
|
0
|
857 ------
|
|
|
858
|
|
|
859 **Citation**
|
|
|
860
|
|
11
|
861 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com
|
|
0
|
862
|
|
4
|
863 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
|
|
0
|
864 </help>
|
|
|
865 </tool>
|
