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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">
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2 <description>
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3 Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.31.4">peptide_shaker</requirement>
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7 <requirement type="package" version="1.19.5">searchgui</requirement>
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8 <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
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9 </requirements>
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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 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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13 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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14 </stdio>
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15 <command>
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16
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17 #from datetime import datetime
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18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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19 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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20 #set $temp_stderr = 'macs2_stderr'
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21
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22 mkdir output;
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23 mkdir output_reports;
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24 cwd=`pwd`;
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25 #for $mgf in $peak_lists:
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26 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
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27 ln -s '${mgf}' '${input_name}';
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28 #end for
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29 ##ln -s "${input_database}" input_database.fasta;
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30 cp "${input_database}" input_database.fasta;
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31
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32 ###########################################
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33 #### Creating decoy database ####
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34 ###########################################
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35 #if $create_decoy:
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36 echo "Creating decoy database.";
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37 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
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38 rm input_database.fasta;
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39 cp input_database_concatenated_target_decoy.fasta input_database.fasta;
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40 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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41 #end if
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42
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43 #####################################################
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44 ## generate IdentificationParameters for SearchGUI ##
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45 #####################################################
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46
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47 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
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48 -out SEARCHGUI_IdentificationParameters.parameters
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49 -prec_ppm "${precursor_ion_tol_units}"
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50 -prec_tol "${precursor_ion_tol}"
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51 -frag_tol "${fragment_tol}"
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52 -enzyme "${enzyme}"
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53 #set $fixed_mods_str = $fixed_modifications or ''
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54 #set $variable_mods_str = $variable_modifications or ''
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55 #if $fixed_mods_str
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56 -fixed_mods "${fixed_mods_str}"
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57 #end if
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58 #if $variable_mods_str
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59 -variable_mods "${variable_mods_str}"
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60 #end if
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61 -min_charge "${min_charge}"
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62 -max_charge "${max_charge}"
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63 -mc "${missed_cleavages}"
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64 -fi "${forward_ion}"
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65 -ri "${reverse_ion}"
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66 -db input_database.fasta
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67
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68 #if $advanced.advanced_type_selector == "advanced":
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69
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70 #if $advanced.xtandem.xtandem_selector == "yes"
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71
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72 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
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73 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
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74 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
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75 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
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76 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
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77
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78 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
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79 -xtandem_refine 1
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80 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
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81 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
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82 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
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83 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
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84 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
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85 #end if
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86 #end if
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87
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88 #if $advanced.omssa.omssa_selector == "yes"
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89 -omssa_hitlist_length ${advanced.omssa.hitlist_length}
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90 -omssa_remove_prec ${advanced.omssa.remove_precursor}
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91 -omssa_scale_prec ${advanced.omssa.scale_precursor}
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92 -omssa_estimate_charge ${advanced.omssa.estimate_charge}
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93 #end if
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94
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95 #if $advanced.msgf.msgf_selector == "yes"
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96 -msgf_decoy ${advanced.msgf.msgf_decoy}
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97 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
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98 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
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99 -msgf_termini ${advanced.msgf.msgf_termini}
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100 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
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101 #end if
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102
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103 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
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104 ##end if
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105
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106 #end if
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107
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108 2> $temp_stderr)
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109 &&
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110
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111 ################
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112 ## Search CLI ##
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113 ################
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114 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
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115 -temp_folder `pwd`
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116 -spectrum_files \$cwd
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117 -output_folder \$cwd/output
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118 -id_params SEARCHGUI_IdentificationParameters.parameters
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119
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120 -threads "\${GALAXY_SLOTS:-12}"
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121 -correct_titles "${correct_titles}"
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122 $missing_titles
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123 -mgf_splitting "${mgf_splitting}"
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124 -mgf_spectrum_count "${mgf_spectrum_count}"
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125
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126 ## 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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127 ## the tree is generated afterwards in PeptideShaker
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128 -protein_index 0
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129
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130 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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131
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132 #if $advanced.advanced_type_selector == "advanced":
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133
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134 #if $advanced.xtandem.xtandem_selector == "yes"
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135 -xtandem 1
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136 #else
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137 -xtandem 0
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138 #end if
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139
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140 #if $advanced.omssa.omssa_selector == "yes"
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141 -omssa 1
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142 #else
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143 -omssa 0
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144 #end if
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145
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146 #if $advanced.msgf.msgf_selector == "yes"
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147 -msgf 1
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148 #else
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149 -msgf 0
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150 #end if
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151
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152 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
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153 -ms_amanda 1
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154 #else
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155 -ms_amanda 0
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156 #end if
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157
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158 #else
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159 -ms_amanda 0
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160 #end if
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161
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162 2>> $temp_stderr)
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163 &&
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164
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165 #########################################################
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166 ## generate IdentificationParameters for PeptideShaker ##
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167 #########################################################
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168 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
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169 -out PEPTIDESHAKER_IdentificationParameters.parameters
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170 -prec_ppm "${precursor_ion_tol_units}"
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171 -prec_tol "${precursor_ion_tol}"
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172 -frag_tol "${fragment_tol}"
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173 -enzyme "${enzyme}"
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174 #set $fixed_mods_str = $fixed_modifications or ''
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175 #set $variable_mods_str = $variable_modifications or ''
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176 #if $fixed_mods_str
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177 -fixed_mods "$fixed_mods_str"
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178 #end if
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179 #if $variable_mods_str
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180 -variable_mods "$variable_mods_str"
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181 #end if
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182 -min_charge $min_charge
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183 -max_charge $max_charge
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184 -mc $missed_cleavages
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185 -fi $forward_ion
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186 -ri $reverse_ion
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187 -db input_database.fasta
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188
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189 2>> $temp_stderr)
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190 &&
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191
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192 ######################
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193 ## PeptideShakerCLI ##
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194 ######################
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195 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
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196 -temp_folder `pwd`
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197 -experiment '${exp_str}'
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198 -sample '${samp_str}'
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199 -replicate 1
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200 -spectrum_files \$cwd
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201 -identification_files \$cwd/output
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202 -out \$cwd/peptide_shaker_output.cps
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203 -id_params PEPTIDESHAKER_IdentificationParameters.parameters
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204
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205 ##Optional gene annotation parameter
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206 #if $species_type.species_type_selector != 'no_species_type':
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207 -species_type "${species_type.species_type_selector}"
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208 -species "${species_type.species}"
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209 #end if
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210
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211 ##Optional processing parameters:
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212 #if $processing_options.processing_options_selector == "yes"
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213 -protein_FDR "${processing_options.protein_fdr}"
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214 -peptide_FDR "${processing_options.peptide_fdr}"
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215 -psm_FDR "${processing_options.psm_fdr}"
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216 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
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217 #if $processing_options.ptm_score.ptm_score_selector == 1
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218 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
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219 #if str($processing_options.ptm_score.ptm_threshold) != ''
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220 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
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221 #end if
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222 #end if
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223 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
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224 #end if
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225
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226 ##Optional filtering parameters:
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227 #if $filtering_options.filtering_options_selector == "yes":
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228 -min_peptide_length "${filtering_options.min_peptide_length}"
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229 -max_peptide_length "${filtering_options.max_peptide_length}"
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230 -max_precursor_error "${filtering_options.max_precursor_error}"
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231 -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
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232 -max_xtandem_e "${filtering_options.max_xtandem_e}"
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233 -max_omssa_e "${filtering_options.max_omssa_e}"
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234 -max_mascot_e "${filtering_options.max_mascot_e}"
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235 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
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236 #end if
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237
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238 2>> $temp_stderr)
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239 &&
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240
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241 ##################################
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242 ## PeptideShaker Report options ##
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243 ##################################
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244 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
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245 -temp_folder `pwd`
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246 -in \$cwd/peptide_shaker_output.cps
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247 -out_reports \$cwd/output_reports
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248 #set $cleaned_list = str($outputs).split(',')
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249 #if 'cps' in $cleaned_list:
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250 #silent $cleaned_list.remove('cps')
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251 #end if
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252 #if 'mzidentML' in $cleaned_list:
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253 #silent $cleaned_list.remove('mzidentML')
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254 #end if
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255 -reports #echo ','.join($cleaned_list)#
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256
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257 2>> $temp_stderr)
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258 &&
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259
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260 #if 'mzidentML' in str($outputs).split(','):
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261 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
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262 -in \$cwd/peptide_shaker_output.cps
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263 -output_file output.mzid
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264 -contact_first_name 'Proteomics'
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265 -contact_last_name 'Galaxy'
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266 -contact_email 'galaxyp@umn.edu'
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267 -contact_address 'galaxyp@umn.edu'
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268 -organization_name 'University of Minnesota'
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269 -organization_email 'galaxyp@umn.edu'
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270 -organization_address 'Minneapolis, MN 55455, Vereinigte Staaten'
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271 ;
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272 #end if
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273 #if '0' in str($outputs).split(','):
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274 find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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275 ;
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276 #end if
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277 #if '2' in str($outputs).split(','):
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278 find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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279 ;
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280 #end if
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281 #if '3' in str($outputs).split(','):
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282 find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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283 ;
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284 #end if
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285 #if '4' in str($outputs).split(','):
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286 find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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287 ;
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288 #end if
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289 #if '1' in str($outputs).split(','):
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290 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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291 ;
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292 #end if
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293
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294 exit_code_for_galaxy=\$?;
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295 cat $temp_stderr 2>&1;
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296 (exit \$exit_code_for_galaxy)
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297
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298 </command>
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299 <inputs>
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300 <param format="fasta" name="input_database" type="data" label="Protein Database"
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301 help="Select FASTA database from history"/>
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302
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303 <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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304
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305 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
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306 help="Select appropriate MGF dataset(s) from history" />
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307 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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308 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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309 <option value="1">Parts per million (ppm)</option>
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310 <option value="0">Daltons</option>
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311 </param>
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312 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
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313 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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314 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
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315 help="Provide error value for fragment ions, based on instrument used"/>
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316 <param name="enzyme" type="select" label="Enzyme"
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317 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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318 <option value="Trypsin">Trypsin</option>
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319 <option value="Arg-C">Arg-C</option>
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320 <option value="CNBr">CNBr</option>
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321 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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322 <option value="Formic Acid">Formic Acid</option>
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323 <option value="Lys-C">Lys-C</option>
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324 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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325 <option value="Pepsin A">Pepsin A</option>
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326 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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327 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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328 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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329 <option value="whole protein">whole protein</option>
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330 <option value="Asp-N">Asp-N</option>
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331 <option value="Glu-C">Glu-C</option>
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332 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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333 <option value="Top-Down">Top-Down</option>
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334 <option value="Semi-Tryptic">Semi-Tryptic</option>
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335 <option value="No enzyme">No enzyme</option>
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336 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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337 <option value="Asp-N (DE)">Asp-N (DE)</option>
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338 <option value="Glu-C (DE)">Glu-C (DE)</option>
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339 <option value="Lys-N (K)">Lys-N (K)</option>
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340 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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341 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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342 <option value="Semi-Glu-C">Semi-Glu-C</option>
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343 </param>
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344
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345 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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346 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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347 <option value="0">no correction</option>
|
|
|
348 <option value="1" selected="True">rename spectra</option>
|
|
|
349 <option value="2">delete spectra</option>
|
|
|
350 </param>
|
|
|
351
|
|
|
352 <param name="missing_titles" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" help="(-missing_titles)"/>
|
|
|
353
|
|
|
354 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
|
|
|
355 help="Choose a smaller value if you are running on a machine with limited memory"/>
|
|
|
356 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
|
|
|
357 help="Choose a smaller value if you are running on a machine with limited memory"/>
|
|
|
358
|
|
|
359 <conditional name="species_type">
|
|
|
360 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
|
|
|
361 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">
|
|
|
362 <option value="Fungi">Fungi</option>
|
|
|
363 <option value="Plants">Plants</option>
|
|
|
364 <option value="Metazoa">Metazoa</option>
|
|
|
365 <option value="Vertebrates">Vertebrates</option>
|
|
|
366 <option value="Protists">Protists</option>
|
|
|
367 <option value="no_species_type" selected="true">No species restriction</option>
|
|
|
368 </param>
|
|
|
369 <when value="Protists">
|
|
|
370 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
|
371 help="">
|
|
|
372 <option value="Albugo laibachii">Albugo laibachii</option>
|
|
|
373 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
|
|
|
374 <option value="Entamoeba histolytica">Entamoeba histolytica</option>
|
|
|
375 <option value="Giardia lamblia">Giardia lamblia</option>
|
|
|
376 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
|
|
|
377 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
|
|
|
378 <option value="Leishmania major">Leishmania major</option>
|
|
|
379 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
|
|
|
380 <option value="Phytophthora infestans">Phytophthora infestans</option>
|
|
|
381 <option value="Phytophthora ramorum">Phytophthora ramorum</option>
|
|
|
382 <option value="Phytophthora sojae">Phytophthora sojae</option>
|
|
|
383 <option value="Plasmodium berghei">Plasmodium berghei</option>
|
|
|
384 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
|
|
|
385 <option value="Plasmodium falciparum">Plasmodium falciparum</option>
|
|
|
386 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
|
|
|
387 <option value="Plasmodium vivax">Plasmodium vivax</option>
|
|
|
388 <option value="Pythium ultimum">Pythium ultimum</option>
|
|
|
389 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
|
|
|
390 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
|
|
|
391 <option value="Toxoplasma gondii">Toxoplasma gondii</option>
|
|
|
392 <option value="Trypanosoma brucei">Trypanosoma brucei</option>
|
|
|
393 </param>
|
|
|
394 </when>
|
|
|
395 <when value="Plants">
|
|
|
396 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
|
397 help="">
|
|
|
398 <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
|
|
|
399 <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
|
|
|
400 <option value="Brachypodium distachyon">Brachypodium distachyon</option>
|
|
|
401 <option value="Brassica rapa genes">Brassica rapa genes</option>
|
|
|
402 <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>
|
|
|
403 <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option>
|
|
|
404 <option value="Glycine max">Glycine max</option>
|
|
|
405 <option value="Hordeum vulgare">Hordeum vulgare</option>
|
|
|
406 <option value="Medicago truncatula">Medicago truncatula</option>
|
|
|
407 <option value="Musa acuminata">Musa acuminata</option>
|
|
|
408 <option value="Oryza brachyantha">Oryza brachyantha</option>
|
|
|
409 <option value="Oryza glaberrima">Oryza glaberrima</option>
|
|
|
410 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
|
|
|
411 <option value="Oryza sativa">Oryza sativa</option>
|
|
|
412 <option value="Physcomitrella patens">Physcomitrella patens</option>
|
|
|
413 <option value="Populus trichocarpa">Populus trichocarpa</option>
|
|
|
414 <option value="Selaginella moellendorffii">Selaginella moellendorffii</option>
|
|
|
415 <option value="Setaria italica">Setaria italica</option>
|
|
|
416 <option value="Solanum lycopersicum">Solanum lycopersicum</option>
|
|
|
417 <option value="Solanum tuberosum">Solanum tuberosum</option>
|
|
|
418 <option value="Sorghum bicolor">Sorghum bicolor</option>
|
|
|
419 <option value="Vitis vinifera">Vitis vinifera</option>
|
|
|
420 <option value="Zea mays">Zea mays</option>
|
|
|
421 </param>
|
|
|
422 </when>
|
|
|
423 <when value="Metazoa">
|
|
|
424 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
|
425 help="">
|
|
|
426 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
|
|
|
427 <option value="Aedes aegypti">Aedes aegypti</option>
|
|
|
428 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
|
|
|
429 <option value="Anopheles darlingi">Anopheles darlingi</option>
|
|
|
430 <option value="Anopheles gambiae">Anopheles gambiae</option>
|
|
|
431 <option value="Apis mellifera">Apis mellifera</option>
|
|
|
432 <option value="Atta cephalotes">Atta cephalotes</option>
|
|
|
433 <option value="Bombyx mori">Bombyx mori</option>
|
|
|
434 <option value="Brugia malayi">Brugia malayi</option>
|
|
|
435 <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option>
|
|
|
436 <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option>
|
|
|
437 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
|
|
|
438 <option value="Caenorhabditis japonica">Caenorhabditis japonica</option>
|
|
|
439 <option value="Caenorhabditis remanei">Caenorhabditis remanei</option>
|
|
|
440 <option value="Culex quinquefasciatus">Culex quinquefasciatus</option>
|
|
|
441 <option value="Danaus plexippus">Danaus plexippus</option>
|
|
|
442 <option value="Daphnia pulex">Daphnia pulex</option>
|
|
|
443 <option value="Drosophila ananassae">Drosophila ananassae</option>
|
|
|
444 <option value="Drosophila erecta">Drosophila erecta</option>
|
|
|
445 <option value="Drosophila grimshawi">Drosophila grimshawi</option>
|
|
|
446 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
|
|
|
447 <option value="Drosophila mojavensis">Drosophila mojavensis</option>
|
|
|
448 <option value="Drosophila persimilis">Drosophila persimilis</option>
|
|
|
449 <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option>
|
|
|
450 <option value="Drosophila sechellia">Drosophila sechellia</option>
|
|
|
451 <option value="Drosophila simulans">Drosophila simulans</option>
|
|
|
452 <option value="Drosophila virilis">Drosophila virilis</option>
|
|
|
453 <option value="Drosophila willistoni">Drosophila willistoni</option>
|
|
|
454 <option value="Drosophila yakuba">Drosophila yakuba</option>
|
|
|
455 <option value="Heliconius melpomene">Heliconius melpomene</option>
|
|
|
456 <option value="Ixodes scapularis">Ixodes scapularis</option>
|
|
|
457 <option value="Loa loa">Loa loa</option>
|
|
|
458 <option value="Megaselia scalaris">Megaselia scalaris</option>
|
|
|
459 <option value="Nasonia vitripennis">Nasonia vitripennis</option>
|
|
|
460 <option value="Nematostella vectensis">Nematostella vectensis</option>
|
|
|
461 <option value="Pediculus humanus">Pediculus humanus</option>
|
|
|
462 <option value="Pristionchus pacificus">Pristionchus pacificus</option>
|
|
|
463 <option value="Schistosoma mansoni">Schistosoma mansoni</option>
|
|
|
464 <option value="Strigamia maritima">Strigamia maritima</option>
|
|
|
465 <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option>
|
|
|
466 <option value="Tribolium castaneum">Tribolium castaneum</option>
|
|
|
467 <option value="Trichinella spiralis">Trichinella spiralis</option>
|
|
|
468 <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
|
|
|
469 </param>
|
|
|
470 </when>
|
|
|
471 <when value="Fungi">
|
|
|
472 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
|
473 help="">
|
|
|
474 <option value="Ashbya gossypii">Ashbya gossypii</option>
|
|
|
475 <option value="Aspergillus clavatus">Aspergillus clavatus</option>
|
|
|
476 <option value="Aspergillus flavus">Aspergillus flavus</option>
|
|
|
477 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
|
|
|
478 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
|
|
|
479 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
|
|
|
480 <option value="Aspergillus niger">Aspergillus niger</option>
|
|
|
481 <option value="Aspergillus oryzae">Aspergillus oryzae</option>
|
|
|
482 <option value="Aspergillus terreus">Aspergillus terreus</option>
|
|
|
483 <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option>
|
|
|
484 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
|
|
|
485 <option value="Fusarium oxysporum">Fusarium oxysporum</option>
|
|
|
486 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
|
|
|
487 <option value="Gibberella moniliformis">Gibberella moniliformis</option>
|
|
|
488 <option value="Gibberella zeae">Gibberella zeae</option>
|
|
|
489 <option value="Glomerella graminicola">Glomerella graminicola</option>
|
|
|
490 <option value="Komagataella pastoris">Komagataella pastoris</option>
|
|
|
491 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
|
|
|
492 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
|
|
|
493 <option value="Magnaporthe poae">Magnaporthe poae</option>
|
|
|
494 <option value="Melampsora larici-populina">Melampsora larici-populina</option>
|
|
|
495 <option value="Nectria haematococca">Nectria haematococca</option>
|
|
|
496 <option value="Neosartorya fischeri">Neosartorya fischeri</option>
|
|
|
497 <option value="Neurospora crassa">Neurospora crassa</option>
|
|
|
498 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
|
|
|
499 <option value="Puccinia graminis">Puccinia graminis</option>
|
|
|
500 <option value="Puccinia triticina">Puccinia triticina</option>
|
|
|
501 <option value="Pyrenophora teres">Pyrenophora teres</option>
|
|
|
502 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
|
|
|
503 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
|
|
|
504 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
|
|
|
505 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
|
|
|
506 <option value="Sporisorium reilianum">Sporisorium reilianum</option>
|
|
|
507 <option value="Trichoderma reesei">Trichoderma reesei</option>
|
|
|
508 <option value="Trichoderma virens">Trichoderma virens</option>
|
|
|
509 <option value="Tuber melanosporum">Tuber melanosporum</option>
|
|
|
510 <option value="Ustilago maydis">Ustilago maydis</option>
|
|
|
511 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
|
|
|
512 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
|
|
|
513 </param>
|
|
|
514 </when>
|
|
|
515 <when value="Vertebrates">
|
|
|
516 <param name="species" type="select" label="The species to use for the gene annotation"
|
|
|
517 help="">
|
|
|
518 <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
|
|
|
519 <option value="Anolis carolinensis">Anolis carolinensis</option>
|
|
|
520 <option value="Bos taurus">Bos taurus</option>
|
|
|
521 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
|
|
|
522 <option value="Callithrix jacchus">Callithrix jacchus</option>
|
|
|
523 <option value="Canis familiaris">Canis familiaris</option>
|
|
|
524 <option value="Cavia porcellus">Cavia porcellus</option>
|
|
|
525 <option value="Choloepus hoffmanni">Choloepus hoffmanni</option>
|
|
|
526 <option value="Ciona intestinalis">Ciona intestinalis</option>
|
|
|
527 <option value="Ciona savignyi">Ciona savignyi</option>
|
|
|
528 <option value="Danio rerio">Danio rerio</option>
|
|
|
529 <option value="Dasypus novemcinctus">Dasypus novemcinctus</option>
|
|
|
530 <option value="Dipodomys ordii">Dipodomys ordii</option>
|
|
|
531 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
|
|
|
532 <option value="Echinops telfairi">Echinops telfairi</option>
|
|
|
533 <option value="Equus caballus">Equus caballus</option>
|
|
|
534 <option value="Erinaceus europaeus">Erinaceus europaeus</option>
|
|
|
535 <option value="Felis catus">Felis catus</option>
|
|
|
536 <option value="Gallus gallus">Gallus gallus</option>
|
|
|
537 <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option>
|
|
|
538 <option value="Gorilla gorilla">Gorilla gorilla</option>
|
|
|
539 <option value="Homo sapiens">Homo sapiens</option>
|
|
|
540 <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option>
|
|
|
541 <option value="Latimeria chalumnae">Latimeria chalumnae</option>
|
|
|
542 <option value="Loxodonta africana">Loxodonta africana</option>
|
|
|
543 <option value="Macaca mulatta">Macaca mulatta</option>
|
|
|
544 <option value="Macropus eugenii">Macropus eugenii</option>
|
|
|
545 <option value="Meleagris gallopavo">Meleagris gallopavo</option>
|
|
|
546 <option value="Microcebus murinus">Microcebus murinus</option>
|
|
|
547 <option value="Monodelphis domestica">Monodelphis domestica</option>
|
|
|
548 <option value="Mus musculus">Mus musculus</option>
|
|
|
549 <option value="Mustela putorius furo">Mustela putorius furo</option>
|
|
|
550 <option value="Myotis lucifugus">Myotis lucifugus</option>
|
|
|
551 <option value="Nomascus leucogenys">Nomascus leucogenys</option>
|
|
|
552 <option value="Ochotona princeps">Ochotona princeps</option>
|
|
|
553 <option value="Oreochromis niloticus">Oreochromis niloticus</option>
|
|
|
554 <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
|
|
|
555 <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
|
|
|
556 <option value="Oryzias latipes">Oryzias latipes</option>
|
|
|
557 <option value="Otolemur garnettii">Otolemur garnettii</option>
|
|
|
558 <option value="Pan troglodytes">Pan troglodytes</option>
|
|
|
559 <option value="Petromyzon marinus">Petromyzon marinus</option>
|
|
|
560 <option value="Pelodiscus sinensis">Pelodiscus sinensis</option>
|
|
|
561 <option value="Pongo abelii">Pongo abelii</option>
|
|
|
562 <option value="Procavia capensis">Procavia capensis</option>
|
|
|
563 <option value="Pteropus vampyrus">Pteropus vampyrus</option>
|
|
|
564 <option value="Rattus norvegicus">Rattus norvegicus</option>
|
|
|
565 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
|
|
|
566 <option value="Sarcophilus harrisii">Sarcophilus harrisii</option>
|
|
|
567 <option value="Sorex araneus">Sorex araneus</option>
|
|
|
568 <option value="Sus scrofa">Sus scrofa</option>
|
|
|
569 <option value="Taeniopygia guttata">Taeniopygia guttata</option>
|
|
|
570 <option value="Takifugu rubripes">Takifugu rubripes</option>
|
|
|
571 <option value="Tarsius syrichta">Tarsius syrichta</option>
|
|
|
572 <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option>
|
|
|
573 <option value="Tupaia belangeri">Tupaia belangeri</option>
|
|
|
574 <option value="Tursiops truncatus">Tursiops truncatus</option>
|
|
|
575 <option value="Vicugna pacos">Vicugna pacos</option>
|
|
|
576 <option value="Xenopus tropicalis">Xenopus tropicalis</option>
|
|
|
577 <option value="Xiphophorus maculatus">Xiphophorus maculatus</option>
|
|
|
578 </param>
|
|
|
579 </when>
|
|
|
580 </conditional>
|
|
|
581
|
|
|
582 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
|
|
|
583 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
|
|
|
584 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
|
|
|
585 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
|
|
|
586 <options from_file="searchgui_mods.loc">
|
|
|
587 <column name="name" index="0" />
|
|
|
588 <column name="value" index="0" />
|
|
|
589 </options>
|
|
|
590 </param>
|
|
|
591 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
|
|
|
592 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
|
|
|
593 <options from_file="searchgui_mods.loc">
|
|
|
594 <column name="name" index="0" />
|
|
|
595 <column name="value" index="0" />
|
|
|
596 </options>
|
|
|
597 </param>
|
|
|
598 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
|
|
|
599 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
|
|
|
600 <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">
|
|
|
601 <option value="a">a</option>
|
|
|
602 <option value="b" selected="true">b</option>
|
|
|
603 <option value="c">c</option>
|
|
|
604 </param>
|
|
|
605 <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">
|
|
|
606 <option value="x">x</option>
|
|
|
607 <option value="y" selected="true">y</option>
|
|
|
608 <option value="z">z</option>
|
|
|
609 </param>
|
|
|
610 <conditional name="advanced">
|
|
|
611 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
|
|
|
612 <option value="basic" selected="True">Basic</option>
|
|
|
613 <option value="advanced">Advanced</option>
|
|
|
614 </param>
|
|
|
615 <when value="basic" />
|
|
|
616 <when value="advanced">
|
|
|
617 <conditional name="xtandem">
|
|
|
618 <param name="xtandem_selector" type="select" label="Run X!Tandem search">
|
|
|
619 <option value="yes" selected="True">Search with X!Tandem</option>
|
|
|
620 <option value="no">No X!Tandem search</option>
|
|
|
621 </param>
|
|
|
622 <when value="no" />
|
|
|
623 <when value="yes">
|
|
|
624 <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
|
|
|
625 <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
|
|
|
626 <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
|
|
|
627 <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
|
|
|
628 <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
|
|
|
629
|
|
|
630 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
|
|
|
631 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
|
|
|
632 <option value="no" selected="True">Don't refine</option>
|
|
|
633 <option value="yes" >Use refinement</option>
|
|
|
634 </param>
|
|
|
635 <when value="no"/>
|
|
|
636 <when value="yes">
|
|
|
637 <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
|
|
|
638 <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
|
|
|
639 <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
|
|
|
640 <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
|
|
|
641 <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
|
|
|
642 </when>
|
|
|
643 </conditional>
|
|
|
644 </when>
|
|
|
645 </conditional>
|
|
|
646
|
|
|
647 <conditional name="omssa">
|
|
|
648 <param name="omssa_selector" type="select" label="Run OMSSA search">
|
|
|
649 <option value="yes" selected="True">Search with OMSSA</option>
|
|
|
650 <option value="no">No OMSSA search</option>
|
|
|
651 </param>
|
|
|
652 <when value="no" />
|
|
|
653 <when value="yes">
|
|
|
654 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
|
|
|
655 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
|
|
|
656 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
|
|
|
657 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
|
|
|
658 </when>
|
|
|
659 </conditional>
|
|
|
660
|
|
|
661 <conditional name="msgf">
|
|
|
662 <param name="msgf_selector" type="select" label="Run MSGF search">
|
|
|
663 <option value="yes" selected="True">Search with MSGF</option>
|
|
|
664 <option value="no">No MSGF search</option>
|
|
|
665 </param>
|
|
|
666 <when value="no" />
|
|
|
667 <when value="yes">
|
|
|
668 <param name="msgf_decoy" label="Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
|
|
|
669 <param name="msgf_min_pep_length" label="Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
|
|
|
670 <param name="msgf_max_pep_length" label="Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
|
|
|
671 <param name="msgf_termini" label="Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
|
|
|
672 <option value="0">0 (ie non-specific cleavage)</option>
|
|
|
673 <option value="1">1 (ie semi-tryptic cleavage)</option>
|
|
|
674 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
|
|
|
675 </param>
|
|
|
676 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
|
|
|
677 </when>
|
|
|
678 </conditional>
|
|
|
679
|
|
|
680 <conditional name="ms_amanda">
|
|
|
681 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
|
|
|
682 <option value="yes">Search with MS Amanda</option>
|
|
|
683 <option value="no" selected="True">No MS Amanda search</option>
|
|
|
684 </param>
|
|
|
685 <when value="no" />
|
|
|
686 <when value="yes">
|
|
|
687 </when>
|
|
|
688 </conditional>
|
|
|
689 </when>
|
|
|
690 </conditional>
|
|
|
691 <conditional name="processing_options">
|
|
|
692 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
|
|
|
693 <option value="no" selected="True">Default Processing Options</option>
|
|
|
694 <option value="yes">Advanced Processing Options</option>
|
|
|
695 </param>
|
|
|
696 <when value="no" />
|
|
|
697 <when value="yes">
|
|
|
698 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
|
699 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
|
700 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
|
|
|
701 <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
|
|
|
702 help="default 95%: '95.0'" />
|
|
|
703 <conditional name="ptm_score">
|
|
|
704 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
|
|
|
705 <option value="0" selected="True">A-score</option>
|
|
|
706 <option value="1">PhosphoRS</option>
|
|
|
707 </param>
|
|
|
708 <when value="0" />
|
|
|
709 <when value="1">
|
|
|
710 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
|
|
|
711 <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
|
|
|
712 help="Automatic mode will be used if not set" />
|
|
|
713 </when>
|
|
|
714 </conditional>
|
|
|
715 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
|
|
|
716 </when>
|
|
|
717 </conditional>
|
|
|
718 <conditional name="filtering_options">
|
|
|
719 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
|
|
|
720 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
|
|
|
721 <option value="no" selected="True">Default Filtering Options</option>
|
|
|
722 <option value="yes">Advanced Processing Options</option>
|
|
|
723 </param>
|
|
|
724 <when value="no" />
|
|
|
725 <when value="yes">
|
|
|
726 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
|
|
|
727 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
|
|
|
728 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" />
|
|
|
729 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
|
|
|
730 <option value="0">ppm</option>
|
|
|
731 <option value="1">Daltons</option>
|
|
|
732 </param>
|
|
|
733 <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
|
|
|
734 <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
|
|
|
735 <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" />
|
|
|
736 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
|
|
|
737 </when>
|
|
|
738 </conditional>
|
|
|
739
|
|
|
740 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
|
|
|
741 <option value="mzidentML" selected="True">mzidentML File</option>
|
|
|
742 <option value="3" selected="True">Peptide Report</option>
|
|
|
743 <option value="4" selected="True">Protein Report</option>
|
|
|
744 <option value="2">PSM Report</option>
|
|
|
745 <option value="0">Certificate of Analysis</option>
|
|
|
746 <option value="1">Hierarchical Report</option>
|
|
|
747 <option value="cps">CPS file</option>
|
|
|
748 <validator type="no_options" message="Please select at least one output file" />
|
|
|
749 </param>
|
|
|
750 </inputs>
|
|
|
751 <outputs>
|
|
|
752 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
|
|
|
753 <filter>'mzidentML' in outputs</filter>
|
|
|
754 </data>
|
|
|
755 <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
|
|
|
756 <filter>'cps' in outputs</filter>
|
|
|
757 </data>
|
|
|
758 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
|
|
|
759 <filter>'0' in outputs</filter>
|
|
|
760 </data>
|
|
|
761 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
|
|
|
762 <filter>'2' in outputs</filter>
|
|
|
763 </data>
|
|
|
764 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
|
|
|
765 <filter>'3' in outputs</filter>
|
|
|
766 </data>
|
|
|
767 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
|
|
|
768 <filter>'4' in outputs</filter>
|
|
|
769 </data>
|
|
|
770 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
|
|
|
771 <filter>'1' in outputs</filter>
|
|
|
772 </data>
|
|
|
773 </outputs>
|
|
|
774 <tests>
|
|
|
775 <test>
|
|
|
776 <param name="input_database" value="tinydb.fasta"/>
|
|
|
777 <param name="peak_lists" value="tinyspectra.mgf"/>
|
|
|
778 <param name="precursor_ion_tol" value="100"/>
|
|
|
779 <param name="fixed_modifications" value="carbamidomethyl c"/>
|
|
|
780 <param name="variable_modifications" value="oxidation of m"/>
|
|
|
781 <param name="min_charge" value="1"/>
|
|
|
782 <param name="max_charge" value="3"/>
|
|
|
783 <param name="advanced_type_selector" value="advanced"/>
|
|
|
784 <param name="species_type_selector" value="no_species_type"/>
|
|
|
785 <param name="processing_options_selector" value="no"/>
|
|
|
786 <param name="filtering_options_selector" value="no"/>
|
|
|
787 <!--param name="xtandem_selector" value="no"/>-->
|
|
|
788 <param name="xtandem_selector" value="yes"/>
|
|
|
789 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
|
|
|
790
|
|
|
791 <param name="omssa_selector" value="no"/>
|
|
|
792 <param name="msgf_selector" value="yes"/>
|
|
|
793 <param name="ms_amanda_selector" value="no"/>
|
|
|
794
|
|
|
795 <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" />
|
|
|
796 </test>
|
|
|
797 </tests>
|
|
|
798 <help>
|
|
|
799 **What it does**
|
|
|
800
|
|
|
801 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
|
|
|
802
|
|
|
803 https://code.google.com/p/peptide-shaker/
|
|
|
804
|
|
|
805 https://code.google.com/p/searchgui/
|
|
|
806
|
|
|
807 ----
|
|
|
808
|
|
|
809 Reports
|
|
|
810 =======
|
|
|
811
|
|
|
812
|
|
|
813 PSM Report
|
|
|
814 ----------
|
|
|
815
|
|
|
816 * Protein(s): Protein(s) to which the peptide can be attached
|
|
|
817 * Sequence: Sequence of the peptide
|
|
|
818 * Variable Modifications: The variable modifications
|
|
|
819 * D-score: D-score for variable PTM localization
|
|
|
820 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
|
|
|
821 * Localization Confidence: The confidence in variable PTM localization.
|
|
|
822 * Fixed Modifications: The fixed modifications.
|
|
|
823 * Spectrum File: The spectrum file.
|
|
|
824 * Spectrum Title: The title of the spectrum.
|
|
|
825 * Spectrum Scan Number: The spectrum scan number.
|
|
|
826 * RT: Retention time
|
|
|
827 * m/z: Measured m/z
|
|
|
828 * Measured Charge: The charge as given in the spectrum file.
|
|
|
829 * Identification Charge: The charge as inferred by the search engine.
|
|
|
830 * Theoretical Mass: The theoretical mass of the peptide.
|
|
|
831 * Isotope Number: The isotope number targetted by the instrument.
|
|
|
832 * Precursor m/z Error: The precursor m/z matching error.
|
|
|
833 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
|
|
|
834 * Confidence: Confidence in percent associated to the retained PSM.
|
|
|
835 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
836 * Validation: Indicates the validation level of the protein group.
|
|
|
837
|
|
|
838
|
|
|
839 Protein Report
|
|
|
840 --------------
|
|
|
841
|
|
|
842 * Main Accession: Main accession of the protein group.
|
|
|
843 * Description: Description of the protein designed by the main accession.
|
|
|
844 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
|
|
|
845 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
|
|
|
846 * PI: Protein Inference status of the protein group.
|
|
|
847 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
|
|
|
848 * Protein Group: The complete protein group (alphabetical order).
|
|
|
849 * #Peptides: Total number of peptides.
|
|
|
850 * #Validated Peptides: Number of validated peptides.
|
|
|
851 * #Unique: Total number of peptides unique to this protein group.
|
|
|
852 * #PSMs: Number of PSMs
|
|
|
853 * #Validated PSMs: Number of validated PSMs
|
|
|
854 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
|
|
|
855 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
|
|
|
856 * MW (kDa): Molecular Weight.
|
|
|
857 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
|
|
|
858 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
|
|
|
859 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
|
|
|
860 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
|
|
|
861 * Score: Score of the protein group.
|
|
|
862 * Confidence: Confidence in percent associated to the protein group.
|
|
|
863 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
|
|
|
864 * Validation: Indicates the validation level of the protein group.
|
|
|
865
|
|
|
866
|
|
|
867 Peptide Report
|
|
|
868 --------------
|
|
|
869
|
|
|
870
|
|
|
871 * Protein(s): Protein(s) to which this peptide can be attached.
|
|
|
872 * AAs Before: The amino-acids before the sequence.
|
|
|
873 * Sequence: Sequence of the peptide.
|
|
|
874 * AAs After: The amino-acids after the sequence.
|
|
|
875 * Modified Sequence: The peptide sequence annotated with variable modifications.
|
|
|
876 * Variable Modifications: The variable modifications.
|
|
|
877 * Localization Confidence: The confidence in PTMs localization.
|
|
|
878 * Fixed Modifications: The fixed modifications.
|
|
|
879 * #Validated PSMs: Number of validated PSMs.
|
|
|
880 * #PSMs: Number of PSMs.
|
|
|
881 * Score: Score of the peptide.
|
|
|
882 * Confidence: Confidence in percent associated to the peptide.
|
|
|
883 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
884 * Validation: Indicates the validation level of the protein group.
|
|
|
885
|
|
|
886
|
|
|
887 Hierachical Report
|
|
|
888 ------------------
|
|
|
889
|
|
|
890 * Main Accession: Main accession of the protein group.
|
|
|
891 * Description: Description of the protein designed by the main accession.
|
|
|
892 * PI: Protein Inference status of the protein group.
|
|
|
893 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
|
|
|
894 * Protein Group: The complete protein group (alphabetical order).
|
|
|
895 * #Peptides: Total number of peptides.
|
|
|
896 * #Validated Peptides: Number of validated peptides.
|
|
|
897 * #Unique: Total number of peptides unique to this protein group.
|
|
|
898 * #PSMs: Number of PSMs
|
|
|
899 * #Validated PSMs: Number of validated PSMs
|
|
|
900 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
|
|
|
901 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
|
|
|
902 * MW (kDa): Molecular Weight.
|
|
|
903 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
|
|
|
904 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
|
|
|
905 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
|
|
|
906 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
|
|
|
907 * Score: Score of the protein group.
|
|
|
908 * Confidence: Confidence in percent associated to the protein group.
|
|
|
909 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
|
|
|
910 * Validation: Indicates the validation level of the protein group.
|
|
|
911 * Protein(s): Protein(s) to which this peptide can be attached.
|
|
|
912 * AAs Before: The amino-acids before the sequence.
|
|
|
913 * Sequence: Sequence of the peptide.
|
|
|
914 * AAs After: The amino-acids after the sequence.
|
|
|
915 * Variable Modifications: The variable modifications.
|
|
|
916 * Localization Confidence: The confidence in PTMs localization.
|
|
|
917 * Fixed Modifications: The fixed modifications.
|
|
|
918 * #Validated PSMs: Number of validated PSMs.
|
|
|
919 * #PSMs: Number of PSMs.
|
|
|
920 * Score: Score of the peptide.
|
|
|
921 * Confidence: Confidence in percent associated to the peptide.
|
|
|
922 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
923 * Validation: Indicates the validation level of the protein group.
|
|
|
924 * Protein(s): Protein(s) to which the peptide can be attached.
|
|
|
925 * Sequence: Sequence of the peptide.
|
|
|
926 * Modified Sequence: The peptide sequence annotated with variable modifications.
|
|
|
927 * Variable Modifications: The variable modifications.
|
|
|
928 * D-score: D-score for variable PTM localization.
|
|
|
929 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
|
|
|
930 * Localization Confidence: The confidence in variable PTM localization.
|
|
|
931 * Fixed Modifications: The fixed modifications.
|
|
|
932 * Spectrum File: The spectrum file.
|
|
|
933 * Spectrum Title: The title of the spectrum.
|
|
|
934 * Spectrum Scan Number: The spectrum scan number.
|
|
|
935 * RT: Retention time
|
|
|
936 * m/z: Measured m/z
|
|
|
937 * Measured Charge: The charge as given in the spectrum file.
|
|
|
938 * Identification Charge: The charge as inferred by the search engine.
|
|
|
939 * Theoretical Mass: The theoretical mass of the peptide.
|
|
|
940 * Isotope Number: The isotope number targetted by the instrument.
|
|
|
941 * Precursor m/z Error: The precursor m/z matching error.
|
|
|
942 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
|
|
|
943 * Confidence: Confidence in percent associated to the retained PSM.
|
|
|
944 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
|
|
|
945 * Validation: Indicates the validation level of the protein group.
|
|
|
946
|
|
|
947
|
|
|
948
|
|
|
949
|
|
|
950 ------
|
|
|
951
|
|
|
952 **Citation**
|
|
|
953
|
|
|
954 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com
|
|
|
955
|
|
|
956 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
|
|
|
957 </help>
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|
|
958 </tool>
|
