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annotate peptide_shaker.xml @ 50:5814883aa217 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f420e6a9af6569a7fe61702c7d273030a36e84dd
author galaxyp
date Thu, 08 Nov 2018 12:23:02 -0500
parents 58a3e6cb2598
children 864bd76db767
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@">
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2 <description>
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3 Perform protein identification using various search engines based on results from SearchGUI
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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 <requirements>
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9 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
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10 </requirements>
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11 <expand macro="stdio" />
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13 <command><![CDATA[
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14 ## When supporting more advanced Galaxy versions: command use_shared_home="false"
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15 #from datetime import datetime
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16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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18 #set $temp_stderr = "peptideshaker_stderr"
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19 #set $bin_dir = "bin"
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22 mkdir output_reports &&
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23 cwd=`pwd` &&
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24 export HOME=\$cwd &&
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26 echo "" > $temp_stderr &&
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28 ln -s '$searchgui_input' searchgui_input.zip &&
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29 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
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32 peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI
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33 --exec_dir="\$cwd/${bin_dir}"
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34 -temp_folder \$cwd/PathSettingsCLI
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35 -log \$cwd/peptideshaker.log &&
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37 #if str($exporting_options.output_reports) != "None"
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38 #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
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39 #else
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40 #set $output_reports_list = set()
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41 #end if
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42
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43 ######################
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44 ## PeptideShakerCLI ##
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45 ######################
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46 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
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47 --exec_dir="\$cwd/${bin_dir}"
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48 -gui 0
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49 -temp_folder \$cwd/PeptideShakerCLI
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50 -experiment '$exp_str'
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51 -sample '$samp_str'
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52 -replicate 1
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53 -identification_files \$cwd/searchgui_input.zip
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54 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
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55 -out \$cwd/peptideshaker_output.cpsx
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56 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
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57 -zip \$cwd/peptideshaker_output.zip
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58 #end if
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59 -threads "\${GALAXY_SLOTS:-12}"
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60
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61 ##Optional processing parameters:
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62 #if $processing_options.processing_options_selector == "yes"
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63 -protein_fdr "${processing_options.protein_fdr}"
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64 -peptide_fdr "${processing_options.peptide_fdr}"
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65 -psm_fdr "${processing_options.psm_fdr}"
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66 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
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67 #if $processing_options.ptm_score.ptm_score_selector == 1
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68 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
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69 #if str($processing_options.ptm_score.ptm_threshold) != ''
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70 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
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71 #end if
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72 #end if
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73 -ptm_alignment "${processing_options.ptm_alignment}"
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74 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
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75 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
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76 #end if
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78 ##Optional filtering parameters:
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79 #if $filtering_options.filtering_options_selector == "yes":
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80 -import_peptide_length_min "${filtering_options.min_peptide_length}"
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81 -import_peptide_length_max "${filtering_options.max_peptide_length}"
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82 -import_precurosor_mz "${filtering_options.max_precursor_error}"
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83 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
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84 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
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85 ##-max_omssa_e "${filtering_options.max_omssa_e}"
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86 ##-max_mascot_e "${filtering_options.max_mascot_e}"
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87 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
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88 #end if
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89
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galaxyp
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90 ##################################
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91 ## mzidCLI options ##
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92 ##################################
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93
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94 #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
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95 -output_file \$cwd/output.mzid
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96 -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
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97 #if $contact_options.contact_options_selector == "yes":
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98 -contact_first_name "$contact_options.contact_first_name"
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galaxyp
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99 -contact_last_name "$contact_options.contact_last_name"
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galaxyp
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100 -contact_email "$contact_options.contact_email"
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galaxyp
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101 -contact_address "$contact_options.contact_address"
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102 #if str($contact_options.contact_url).strip() != '':
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103 -contact_url = "$contact_options.contact_url"
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104 #end if
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105 -organization_name "$contact_options.organization_name"
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galaxyp
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106 -organization_email "$contact_options.organization_email"
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107 -organization_address "$contact_options.organization_address"
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108 #if str($contact_options.organization_url).strip() != '':
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109 -organization_url = "$contact_options.organization_url"
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110 #end if
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111 #else:
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112 -contact_first_name "Proteomics"
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113 -contact_last_name "Galaxy"
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114 -contact_email "galaxyp@umn.edu"
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115 -contact_address "galaxyp@umn.edu"
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116 -organization_name "University of Minnesota"
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117 -organization_email "galaxyp@umn.edu"
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118 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
18
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119 #end if
49
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120 #end if
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121
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122 ##################################
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123 ## PeptideShaker Report options ##
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124 ##################################
49
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125 ## Generate Reports if the user has selected one of the 11 additional reports
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126 #if len($output_reports_list) > 0
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127 -out_reports \$cwd/output_reports
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128 -reports #echo ','.join($output_reports_list)#
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129 #end if
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130
49
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131 2>> $temp_stderr)
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132
49
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133 #if len(output_reports_list)>0:
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134 #if '0' in $output_reports_list:
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135 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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136 #end if
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137 #if '1' in $output_reports_list:
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138 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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139 #end if
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140 #if '2' in $output_reports_list:
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141 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
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142 #end if`
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143 #if '3' in $output_reports_list:
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144 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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145 #end if
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146 #if '4' in $output_reports_list:
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147 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;
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148 #end if
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149 #if '5' in $output_reports_list:
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150 && find \$cwd/output_reports -name '*Default_Peptide_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
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151 #end if
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152 #if '6' in $output_reports_list:
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153 && find \$cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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154 #end if
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155 #if '7' in $output_reports_list:
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156 && find \$cwd/output_reports -name '*Default_Peptide_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "peptides_nonvalidated.txt"' {} \;
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galaxyp
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157 #end if
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158 #if '8' in $output_reports_list:
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159 && find \$cwd/output_reports -name '*Default_Protein_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
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galaxyp
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160 #end if
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161 #if '9' in $output_reports_list:
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162 && find \$cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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galaxyp
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163 #end if
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164 #if '10' in $output_reports_list:
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165 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
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166 #end if
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167 #if '11' in $output_reports_list:
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168 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
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169 #end if
20
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iracooke
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170 #end if
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iracooke
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171
49
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172 && cat $temp_stderr 2>&1;
20
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173 ]]>
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174 </command>
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175 <inputs>
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176 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
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177 help="SearchGUI Results from History">
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178 <options options_filter_attribute="metadata.searchgui_major_version" >
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179 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
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180 </options>
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181 </param>
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182 <conditional name="processing_options">
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183 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
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184 <option value="no" selected="True">Default Processing Options</option>
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185 <option value="yes">Advanced Processing Options</option>
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186 </param>
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187 <when value="no" />
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188 <when value="yes">
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189 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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190 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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191 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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192 <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
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193 help="default 95%: '95.0'" />
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194 <conditional name="ptm_score">
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195 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
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196 <option value="0" selected="True">A-score</option>
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197 <option value="1">PhosphoRS</option>
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198 <option value="2">None</option>
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199 </param>
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200 <when value="0" />
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201 <when value="1">
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202 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
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203 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
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204 help="Automatic mode will be used if not set" />
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205 </when>
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206 <when value="2" />
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207 </conditional>
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208 <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
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209 <option value="0">Character Sequence</option>
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210 <option value="1" selected="true">Amino Acids</option>
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211 <option value="2">Indistinguishable Amino Acids</option>
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212 </param>
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213 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
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214 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
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215 </when>
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216 </conditional>
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217 <conditional name="filtering_options">
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218 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
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219 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
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220 <option value="no" selected="True">Default Filtering Options</option>
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221 <option value="yes">Advanced Filtering Options</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="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
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226 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
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227 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
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228 help="Next option specifies units (Da or ppm)" />
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229 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
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230 <option value="1">ppm</option>
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231 <option value="0">Daltons</option>
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232 </param>
20
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233 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
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234 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
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235 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
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236 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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237 </when>
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238 </conditional>
30
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239 <conditional name="contact_options">
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240 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
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241 help="Create a Galaxy workflow to save these values">
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242 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
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243 <option value="yes">Specify Contact Information</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="contact_first_name" type="text" value="" label="Contact first name.">
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248 <validator type="regex" message="">\S+.*</validator>
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249 </param>
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250 <param name="contact_last_name" type="text" value="" label="Contact last name.">
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251 <validator type="regex" message="">\S+.*</validator>
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252 </param>
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253 <param name="contact_email" type="text" value="" label="Contact e-mail.">
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254 <validator type="regex" message="">\S+@\S+</validator>
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255 </param>
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256 <param name="contact_address" type="text" value="" label="Contact address.">
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257 <validator type="regex" message="">\S+.*</validator>
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258 </param>
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259 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
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260 </param>
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261 <param name="organization_name" type="text" value="" label="Organization name.">
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262 <validator type="regex" message="">\S+.*</validator>
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263 </param>
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264 <param name="organization_email" type="text" value="" label="Organization e-mail.">
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265 <validator type="regex" message="">\S+@\S+</validator>
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266 </param>
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267 <param name="organization_address" type="text" value="" label="Organization address.">
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268 <validator type="regex" message="">\S+.*</validator>
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269 </param>
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270 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
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271 </param>
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272 </when>
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273 </conditional>
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274
49
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275 <section name="exporting_options" expanded="true" title="Exporting options">
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276
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277 <conditional name="mzidentml_conditional">
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278 <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
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279 <when value="1">
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280 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
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281 </when>
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282 <when value="0" />
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283 </conditional>
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284
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285 <conditional name="zip_conditional">
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286 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
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287 <when value="separate">
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288 <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />
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289 </when>
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290 <when value="zip" />
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291 </conditional>
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292
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293 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">
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294 <option value="3">PSM Report</option>
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295 <option value="4">PSM Report with non-validated matches</option>
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296 <option value="2">PSM Phosphorylation Report</option>
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297 <option value="11">Extended PSM Report</option>
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298 <option value="6">Peptide Report</option>
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299 <option value="7">Peptide Report with non-validated matches</option>
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300 <option value="5">Peptide Phosphorylation Report</option>
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301 <option value="9">Protein Report</option>
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302 <option value="10">Protein Report with non-validated matches</option>
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303 <option value="8">Protein Phosphorylation Report</option>
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304 <option value="0">Certificate of Analysis</option>
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305 <option value="1">Hierarchical Report</option>
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306 </param>
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307
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308 </section>
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309
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310 </inputs>
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311 <outputs>
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312 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
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313 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and mzidentml_conditional['mzidentml_creation'] is True</filter>
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314 </data>
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315 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
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316 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter>
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317 </data>
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318 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
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319 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
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320 </data>
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321 <!--
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322 <data format="tabular" name="reports">
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323 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" />
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324 </data>
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325 -->
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326 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
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327 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter>
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328 </data>
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329 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
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330 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter>
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331 </data>
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332 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
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333 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter>
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334 </data>
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335 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
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336 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter>
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337 </data>
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338 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
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339 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter>
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340 </data>
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341 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
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342 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter>
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343 </data>
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344 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
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345 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter>
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346 </data>
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347 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
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348 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter>
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349 </data>
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350 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
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351 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter>
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352 </data>
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353 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
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354 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter>
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355 </data>
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356 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
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357 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter>
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358 </data>
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359 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">
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360 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter>
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361 </data>
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362 </outputs>
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363 <tests>
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364 <test>
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365 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
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366 <param name="processing_options_selector" value="no"/>
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367 <param name="filtering_options_selector" value="no"/>
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368 <param name="mzidentml_creation" value="0"/>
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369 <param name="zip_output_boolean" value="zip"/>
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370 <param name="export_cps" value="1"/>
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371 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
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372 </test>
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373 <test>
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374 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
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375 <param name="processing_options_selector" value="no"/>
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376 <param name="filtering_options_selector" value="yes"/>
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377 <param name="min_peptide_length" value="1"/>
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378 <param name="mzidentml_creation" value="0"/>
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379 <param name="zip_output_boolean" value="separate"/>
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380 <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
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381 <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="8"/>
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382 <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/>
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383 <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/>
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384 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
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385 <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/>
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386 <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/>
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387 <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/>
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388 <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/>
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389 <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>
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390 <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>
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391 <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>
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392 <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>
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393 </test>
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394 <test>
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395 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
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396 <param name="processing_options_selector" value="no"/>
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397 <param name="filtering_options_selector" value="no"/>
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398 <param name="mzidentml_creation" value="0"/>
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399 <param name="zip_output_boolean" value="separate"/>
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400 <param name="export_cps" value="1"/>
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401 <param name="output_reports" value="3"/>
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402 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
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403 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
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404 </test>
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405 </tests>
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406 <help>
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407 **What it does**
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408
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409 PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.
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410
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411 http://compomics.github.io/projects/peptide-shaker.html
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412
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413 ----
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414
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415 Reports
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416 =======
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417
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418
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419 PSM Report
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420 ----------
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421
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422 * Protein(s): Protein(s) to which the peptide can be attached
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423 * Sequence: Sequence of the peptide
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424 * Variable Modifications: The variable modifications
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425 * D-score: D-score for variable PTM localization
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426 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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427 * Localization Confidence: The confidence in variable PTM localization.
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428 * Fixed Modifications: The fixed modifications.
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429 * Spectrum File: The spectrum file.
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430 * Spectrum Title: The title of the spectrum.
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431 * Spectrum Scan Number: The spectrum scan number.
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432 * RT: Retention time
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433 * m/z: Measured m/z
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434 * Measured Charge: The charge as given in the spectrum file.
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435 * Identification Charge: The charge as inferred by the search engine.
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436 * Theoretical Mass: The theoretical mass of the peptide.
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437 * Isotope Number: The isotope number targetted by the instrument.
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438 * Precursor m/z Error: The precursor m/z matching error.
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439 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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440 * Confidence: Confidence in percent associated to the retained PSM.
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441 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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442 * Validation: Indicates the validation level of the protein group.
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443
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444
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445 Protein Report
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446 --------------
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447
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448 * Main Accession: Main accession of the protein group.
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449 * Description: Description of the protein designed by the main accession.
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450 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
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451 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
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452 * PI: Protein Inference status of the protein group.
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453 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
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454 * Protein Group: The complete protein group (alphabetical order).
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455 * #Peptides: Total number of peptides.
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456 * #Validated Peptides: Number of validated peptides.
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457 * #Unique: Total number of peptides unique to this protein group.
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458 * #PSMs: Number of PSMs
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459 * #Validated PSMs: Number of validated PSMs
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460 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
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461 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
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462 * MW (kDa): Molecular Weight.
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463 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
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464 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
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465 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
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466 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
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467 * Score: Score of the protein group.
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468 * Confidence: Confidence in percent associated to the protein group.
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469 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
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470 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
471
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iracooke
parents:
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472
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iracooke
parents:
diff changeset
473 Peptide Report
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iracooke
parents:
diff changeset
474 --------------
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iracooke
parents:
diff changeset
475
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iracooke
parents:
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476
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iracooke
parents:
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477 * Protein(s): Protein(s) to which this peptide can be attached.
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iracooke
parents:
diff changeset
478 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
479 * Sequence: Sequence of the peptide.
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iracooke
parents:
diff changeset
480 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
481 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
482 * Variable Modifications: The variable modifications.
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iracooke
parents:
diff changeset
483 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
484 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
diff changeset
485 * #Validated PSMs: Number of validated PSMs.
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iracooke
parents:
diff changeset
486 * #PSMs: Number of PSMs.
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iracooke
parents:
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487 * Score: Score of the peptide.
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iracooke
parents:
diff changeset
488 * Confidence: Confidence in percent associated to the peptide.
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iracooke
parents:
diff changeset
489 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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iracooke
parents:
diff changeset
490 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
491
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
492
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iracooke
parents:
diff changeset
493 Hierachical Report
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iracooke
parents:
diff changeset
494 ------------------
a5f9b959d5d1 Uploaded
iracooke
parents:
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495
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iracooke
parents:
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496 * Main Accession: Main accession of the protein group.
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iracooke
parents:
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497 * Description: Description of the protein designed by the main accession.
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iracooke
parents:
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498 * PI: Protein Inference status of the protein group.
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iracooke
parents:
diff changeset
499 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
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iracooke
parents:
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500 * Protein Group: The complete protein group (alphabetical order).
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iracooke
parents:
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501 * #Peptides: Total number of peptides.
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iracooke
parents:
diff changeset
502 * #Validated Peptides: Number of validated peptides.
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iracooke
parents:
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503 * #Unique: Total number of peptides unique to this protein group.
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iracooke
parents:
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504 * #PSMs: Number of PSMs
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iracooke
parents:
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505 * #Validated PSMs: Number of validated PSMs
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iracooke
parents:
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506 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
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iracooke
parents:
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507 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
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iracooke
parents:
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508 * MW (kDa): Molecular Weight.
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iracooke
parents:
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509 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
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iracooke
parents:
diff changeset
510 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
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iracooke
parents:
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511 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
512 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
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iracooke
parents:
diff changeset
513 * Score: Score of the protein group.
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iracooke
parents:
diff changeset
514 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
515 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
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iracooke
parents:
diff changeset
516 * Validation: Indicates the validation level of the protein group.
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iracooke
parents:
diff changeset
517 * Protein(s): Protein(s) to which this peptide can be attached.
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iracooke
parents:
diff changeset
518 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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519 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
520 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
521 * Variable Modifications: The variable modifications.
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iracooke
parents:
diff changeset
522 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
523 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
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524 * #Validated PSMs: Number of validated PSMs.
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iracooke
parents:
diff changeset
525 * #PSMs: Number of PSMs.
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iracooke
parents:
diff changeset
526 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
527 * Confidence: Confidence in percent associated to the peptide.
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iracooke
parents:
diff changeset
528 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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iracooke
parents:
diff changeset
529 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
530 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
531 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
532 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
533 * Variable Modifications: The variable modifications.
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iracooke
parents:
diff changeset
534 * D-score: D-score for variable PTM localization.
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iracooke
parents:
diff changeset
535 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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iracooke
parents:
diff changeset
536 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
537 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
diff changeset
538 * Spectrum File: The spectrum file.
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iracooke
parents:
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539 * Spectrum Title: The title of the spectrum.
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iracooke
parents:
diff changeset
540 * Spectrum Scan Number: The spectrum scan number.
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iracooke
parents:
diff changeset
541 * RT: Retention time
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iracooke
parents:
diff changeset
542 * m/z: Measured m/z
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iracooke
parents:
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543 * Measured Charge: The charge as given in the spectrum file.
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iracooke
parents:
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544 * Identification Charge: The charge as inferred by the search engine.
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iracooke
parents:
diff changeset
545 * Theoretical Mass: The theoretical mass of the peptide.
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iracooke
parents:
diff changeset
546 * Isotope Number: The isotope number targetted by the instrument.
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iracooke
parents:
diff changeset
547 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
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548 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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iracooke
parents:
diff changeset
549 * Confidence: Confidence in percent associated to the retained PSM.
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iracooke
parents:
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550 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
551 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
552
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iracooke
parents:
diff changeset
553
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
554 ------
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iracooke
parents:
diff changeset
555
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
556 **Citation**
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
557
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
558 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
18
a5f9b959d5d1 Uploaded
iracooke
parents:
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559
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
560 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18
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iracooke
parents:
diff changeset
561 </help>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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diff changeset
562 <expand macro="citations" />
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iracooke
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563 </tool>