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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.23.0">
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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 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <command>
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11 <![CDATA[
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12 #from datetime import datetime
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13 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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14 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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15 #set $temp_stderr = 'macs2_stderr'
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16
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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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44
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45 @GENERAL_PARAMETERS@
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46
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47 -db input_database.fasta
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48
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49 #if $advanced.advanced_type_selector == "advanced":
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50
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51 #if $advanced.xtandem.xtandem_selector == "yes"
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52
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53 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
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54 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
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55 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
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56 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
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57 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
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58
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59 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
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60 -xtandem_refine 1
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61 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
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62 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
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63 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
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64 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
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65 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
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66 #end if
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67 #end if
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68
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69 #if $advanced.omssa.omssa_selector == "yes"
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70 -omssa_hitlist_length ${advanced.omssa.hitlist_length}
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71 -omssa_remove_prec ${advanced.omssa.remove_precursor}
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72 -omssa_scale_prec ${advanced.omssa.scale_precursor}
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73 -omssa_estimate_charge ${advanced.omssa.estimate_charge}
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74 #end if
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75
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76 #if $advanced.msgf.msgf_selector == "yes"
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77 -msgf_decoy ${advanced.msgf.msgf_decoy}
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78 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
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79 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
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80 -msgf_termini ${advanced.msgf.msgf_termini}
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81 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
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82 #end if
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83
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84 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
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85 ##end if
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86
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87 #end if
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88
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89 2> $temp_stderr)
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90 &&
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91
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92 ################
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93 ## Search CLI ##
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94 ################
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95 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
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96 -temp_folder `pwd`
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97 -spectrum_files \$cwd
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98 -output_folder \$cwd/output
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99 -id_params SEARCHGUI_IdentificationParameters.parameters
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100
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101 -threads "\${GALAXY_SLOTS:-12}"
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102 -correct_titles "${correct_titles}"
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103 $missing_titles
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104 -mgf_splitting "${mgf_splitting}"
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105 -mgf_spectrum_count "${mgf_spectrum_count}"
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106
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107 ## 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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108 ## the tree is generated afterwards in PeptideShaker
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109 -protein_index 0
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110
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111 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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112
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113 #if $advanced.advanced_type_selector == "advanced":
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114
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115 #if $advanced.xtandem.xtandem_selector == "yes"
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116 -xtandem 1
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117 #else
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118 -xtandem 0
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119 #end if
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120
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121 #if $advanced.omssa.omssa_selector == "yes"
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122 -omssa 1
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123 #else
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124 -omssa 0
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125 #end if
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126
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127 #if $advanced.msgf.msgf_selector == "yes"
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128 -msgf 1
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129 #else
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130 -msgf 0
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131 #end if
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132
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133 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
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134 -ms_amanda 1
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135 #else
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136 -ms_amanda 0
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137 #end if
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138
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139 #if $advanced.myrimatch.myrimatch_selector == "yes"
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140 -myrimatch 1
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141 #else
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142 -myrimatch 0
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143 #end if
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144
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145 #if $advanced.comet.comet_selector == "yes"
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146 -comet 1
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147 #else
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148 -comet 0
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149 #end if
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150
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151 #else
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152 -ms_amanda 0
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153 #end if
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154
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155 ## single zip file
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156 -output_option 0
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157
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158 2>> $temp_stderr)
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159
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160 &&
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161
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162 exit_code_for_galaxy=\$?;
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163 cat $temp_stderr 2>&1;
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164 (exit \$exit_code_for_galaxy)
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165 ]]>
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166 </command>
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167 <inputs>
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168 <param format="fasta" name="input_database" type="data" label="Protein Database"
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169 help="Select FASTA database from history"/>
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170
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171 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
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172 label="Create a concatenated target/decoy database before running PeptideShaker"
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173 help="Selecting this option will help PeptideShaker calculate FDR values" />
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174
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175 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
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176 help="Select appropriate MGF dataset(s) from history" />
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177
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178 <expand macro="general_options"/>
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179
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180 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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181 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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182 <option value="0">no correction</option>
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183 <option value="1" selected="True">rename spectra</option>
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184 <option value="2">delete spectra</option>
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185 </param>
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186
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187 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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188 label="Add missing spectrum titles" help="(-missing_titles)"/>
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189
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190 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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191 help="Choose a smaller value if you are running on a machine with limited memory"/>
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192
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193 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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194 help="Choose a smaller value if you are running on a machine with limited memory"/>
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195
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196 <conditional name="advanced">
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197 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
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198 <option value="basic" selected="True">Basic</option>
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199 <option value="advanced">Advanced</option>
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200 </param>
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201 <when value="basic" />
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202 <when value="advanced">
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203 <conditional name="xtandem">
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204 <param name="xtandem_selector" type="select" label="Run X!Tandem search">
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205 <option value="yes" selected="True">Search with X!Tandem</option>
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206 <option value="no">No X!Tandem search</option>
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207 </param>
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208 <when value="no" />
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209 <when value="yes">
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210 <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
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211 <param name="xtandem_min_peaks" type="integer" value="15"
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212 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
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213 <param name="xtandem_min_frag_mz" type="integer" value="200"
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214 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
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215 <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"/>
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216 <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
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217
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218 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
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219 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
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220 <option value="no" selected="True">Don't refine</option>
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221 <option value="yes" >Use refinement</option>
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222 </param>
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223 <when value="no"/>
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224 <when value="yes">
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225 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0"
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226 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
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227 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0"
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228 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
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229 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0"
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230 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
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231 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0"
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232 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
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233 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0"
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234 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
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235 </when>
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236 </conditional>
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237 </when>
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238 </conditional>
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239
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240 <conditional name="omssa">
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241 <param name="omssa_selector" type="select" label="Run OMSSA search">
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242 <option value="yes" selected="True">Search with OMSSA</option>
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243 <option value="no">No OMSSA search</option>
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244 </param>
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245 <when value="no" />
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246 <when value="yes">
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247 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
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248 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
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249 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
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250 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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251 </when>
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252 </conditional>
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253
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254 <conditional name="msgf">
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255 <param name="msgf_selector" type="select" label="Run MSGF search">
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256 <option value="yes" selected="True">Search with MSGF</option>
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257 <option value="no">No MSGF search</option>
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258 </param>
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259 <when value="no" />
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260 <when value="yes">
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261 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0"
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262 label="Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
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263 <param name="msgf_min_pep_length" type="integer" value="6"
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264 label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
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265 <param name="msgf_max_pep_length" type="integer" value="30"
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266 label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
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267 <param name="msgf_termini" type="select" format="text"
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268 label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
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269 <option value="0">0 (ie non-specific cleavage)</option>
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270 <option value="1">1 (ie semi-tryptic cleavage)</option>
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271 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
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272 </param>
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273 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
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274 </when>
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275 </conditional>
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276
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277 <conditional name="ms_amanda">
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278 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
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279 <option value="yes">Search with MS Amanda</option>
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280 <option value="no" selected="True">No MS Amanda search</option>
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281 </param>
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282 <when value="no" />
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283 <when value="yes">
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284 </when>
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285 </conditional>
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286
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287 <conditional name="myrimatch">
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288 <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
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289 <option value="yes">Search with MyriMatch</option>
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290 <option value="no" selected="True">No MyriMatch search</option>
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291 </param>
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292 <when value="no" />
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293 <when value="yes">
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294 </when>
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295 </conditional>
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296
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297 <conditional name="comet">
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298 <param name="comet_selector" type="select" label="Run Comet search">
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299 <option value="yes">Search with Comet</option>
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300 <option value="no" selected="True">No Comet search</option>
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301 </param>
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302 <when value="no" />
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303 <when value="yes">
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304 </when>
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305 </conditional>
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306
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307 </when>
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308 </conditional>
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309
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310 </inputs>
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311 <outputs>
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312 <data format="bgzip" name="searchgui_results" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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313 </outputs>
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314 <tests>
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315 <test>
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316 <param name="input_database" value="tinydb.fasta"/>
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317 <param name="peak_lists" value="tinyspectra.mgf"/>
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318 <param name="precursor_ion_tol" value="100"/>
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319 <param name="fixed_modifications" value="carbamidomethyl c"/>
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320 <param name="variable_modifications" value="oxidation of m"/>
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321 <param name="min_charge" value="1"/>
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322 <param name="max_charge" value="3"/>
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323 <param name="advanced_type_selector" value="advanced"/>
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324 <!--param name="xtandem_selector" value="no"/>-->
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325 <param name="xtandem_selector" value="yes"/>
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326 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
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327
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328 <param name="omssa_selector" value="no"/>
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329 <param name="msgf_selector" value="yes"/>
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330 <param name="ms_amanda_selector" value="no"/>
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331
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332 <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" />
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333 </test>
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334 </tests>
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335 <help>
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336 **What it does**
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337
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338 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI.
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339
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340
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341 </help>
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342 <expand macro="citations" />
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343 </tool>
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