Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 34:0ebf3d3e4c90 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5d191d65c509c913be62ec5b98328c7f36262fbc
author galaxyp
date Thu, 16 Feb 2017 07:37:26 -0500
parents bce45e9e6d70
children bced7eb9e197
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galaxyp
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.15.1">
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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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iracooke
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5 <macros>
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iracooke
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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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galaxyp
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9 <requirement type="package" version="1.15.1">peptide-shaker</requirement>
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10 </requirements>
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11 <expand macro="stdio" />
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12 <command>
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13 <![CDATA[
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14 #from datetime import datetime
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15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 #set $temp_stderr = "peptideshaker_stderr"
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18 #set $bin_dir = "bin"
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20
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21 mkdir output_reports;
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22 cwd=`pwd`;
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23
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24 ln -s '$searchgui_input' searchgui_input.zip &&
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25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
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26 ######################
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27 ## PeptideShakerCLI ##
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28 ######################
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29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
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30 --exec_dir="\$cwd/${bin_dir}"
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31 -temp_folder \$cwd/PeptideShakerCLI
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32 -experiment '$exp_str'
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33 -sample '$samp_str'
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34 -replicate 1
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35 -identification_files \$cwd/searchgui_input.zip
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galaxyp
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36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
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37 -out \$cwd/peptideshaker_output.cpsx
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38 -zip \$cwd/peptideshaker_output.zip
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40 -threads "\${GALAXY_SLOTS:-12}"
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41
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42 ##Optional processing parameters:
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43 #if $processing_options.processing_options_selector == "yes"
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44 -protein_fdr "${processing_options.protein_fdr}"
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galaxyp
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45 -peptide_fdr "${processing_options.peptide_fdr}"
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galaxyp
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46 -psm_fdr "${processing_options.psm_fdr}"
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47 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
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48 #if $processing_options.ptm_score.ptm_score_selector == 1
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49 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
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50 #if str($processing_options.ptm_score.ptm_threshold) != ''
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51 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
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52 #end if
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53 #end if
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54 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
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55 -ptm_alignment "${processing_options.ptm_alignment}"
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56 #end if
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57
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58 ##Optional filtering parameters:
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59 #if $filtering_options.filtering_options_selector == "yes":
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60 -import_peptide_length_min "${filtering_options.min_peptide_length}"
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galaxyp
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61 -import_peptide_length_max "${filtering_options.max_peptide_length}"
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62 -import_precurosor_mz "${filtering_options.max_precursor_error}"
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63 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
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64 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
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65 ##-max_omssa_e "${filtering_options.max_omssa_e}"
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66 ##-max_mascot_e "${filtering_options.max_mascot_e}"
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67 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
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68 #end if
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69
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70 2>> $temp_stderr)
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72 &&
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74 echo "Running Reports";
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76 ##################################
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77 ## PeptideShaker Report options ##
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78 ##################################
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79
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80 #if 'mzidentML' in str($outputs).split(','):
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81 echo "Generating mzIdentML";
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galaxyp
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82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
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83 --exec_dir="\$cwd/${bin_dir}"
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84 -in \$cwd/peptideshaker_output.zip
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85 -output_file \$cwd/output.mzid
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86 #if $contact_options.contact_options_selector == "yes":
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galaxyp
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87 -contact_first_name "$contact_options.contact_first_name"
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88 -contact_last_name "$contact_options.contact_last_name"
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89 -contact_email "$contact_options.contact_email"
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galaxyp
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90 -contact_address "$contact_options.contact_address"
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91 #if str($contact_options.contact_url).strip() != '':
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galaxyp
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92 -contact_url = "$contact_options.contact_url"
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93 #end if
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94 -organization_name "$contact_options.organization_name"
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galaxyp
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95 -organization_email "$contact_options.organization_email"
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galaxyp
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96 -organization_address "$contact_options.organization_address"
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galaxyp
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97 #if str($contact_options.organization_url).strip() != '':
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galaxyp
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98 -organization_url = "$contact_options.organization_url"
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99 #end if
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100 #else:
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101 -contact_first_name "Proteomics"
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102 -contact_last_name "Galaxy"
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103 -contact_email "galaxyp@umn.edu"
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104 -contact_address "galaxyp@umn.edu"
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105 -organization_name "University of Minnesota"
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106 -organization_email "galaxyp@umn.edu"
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107 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
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108 #end if
20
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109 2>> $temp_stderr)
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110 &&
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111 #end if
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112
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113 ## Generate Reports if the user has selected one of the 8 additional reports
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114 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
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115 ## and will not be passed to the command line
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116 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
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117
30
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118 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
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119 --exec_dir="\$cwd/${bin_dir}"
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120 -temp_folder \$cwd/ReportCLI
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121 -in \$cwd/peptideshaker_output.zip
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122 -out_reports \$cwd/output_reports
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123 #set $cleaned_list = str($outputs).split(',')
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124 #if 'cps' in $cleaned_list:
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125 #silent $cleaned_list.remove('cps')
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126 #end if
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127 #if 'mzidentML' in $cleaned_list:
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128 #silent $cleaned_list.remove('mzidentML')
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129 #end if
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130 #if 'zip' in $cleaned_list:
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131 #silent $cleaned_list.remove('zip')
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132 #end if
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133 ## Only numbers are left over. These corresponds to different reports.
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134 -reports #echo ','.join($cleaned_list)#
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135
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136 2>> $temp_stderr)
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137 &&
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138 #end if
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139
30
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140 ## # ls -l \$cwd/output_reports/* ;
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141
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142 #if '0' in str($outputs).split(','):
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143 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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144 ;
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145 #end if
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146 #if '1' in str($outputs).split(','):
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147 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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148 ;
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149 #end if
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150 #if '2' in str($outputs).split(','):
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151 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
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152 ;
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153 #end if
30
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154 #if '8' in str($outputs).split(','):
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155 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
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156 ;
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157 #end if
20
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158 #if '3' in str($outputs).split(','):
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159 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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160 ;
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161 #end if
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162 #if '4' in str($outputs).split(','):
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163 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
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164 ;
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165 #end if
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166 #if '5' in str($outputs).split(','):
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167 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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168 ;
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169 #end if
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170 #if '6' in str($outputs).split(','):
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171 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
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172 ;
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173 #end if
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174 #if '7' in str($outputs).split(','):
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175 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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176 ;
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177 #end if
18
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178
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179 exit_code_for_galaxy=\$?;
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180 cat $temp_stderr 2>&1;
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181 (exit \$exit_code_for_galaxy)
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182
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183 ]]>
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184 </command>
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185 <inputs>
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186 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
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187 help="SearchGUI Results from History">
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188 <options options_filter_attribute="metadata.searchgui_major_version" >
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189 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
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190 </options>
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191 </param>
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192 <conditional name="processing_options">
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193 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
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194 <option value="no" selected="True">Default Processing Options</option>
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195 <option value="yes">Advanced Processing Options</option>
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196 </param>
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197 <when value="no" />
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198 <when value="yes">
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199 <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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200 <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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201 <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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202 <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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203 help="default 95%: '95.0'" />
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204 <conditional name="ptm_score">
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205 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
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206 <option value="0" selected="True">A-score</option>
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207 <option value="1">PhosphoRS</option>
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208 </param>
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209 <when value="0" />
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210 <when value="1">
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211 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
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212 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
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213 help="Automatic mode will be used if not set" />
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214 </when>
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215 </conditional>
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216 <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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217 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
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218 </when>
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219 </conditional>
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220 <conditional name="filtering_options">
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221 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
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222 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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223 <option value="no" selected="True">Default Filtering Options</option>
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224 <option value="yes">Advanced Filtering Options</option>
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225 </param>
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226 <when value="no" />
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227 <when value="yes">
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228 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
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229 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
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230 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
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231 help="Next option specifies units (Da or ppm)" />
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232 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
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233 <option value="1">ppm</option>
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234 <option value="0">Daltons</option>
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235 </param>
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236 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
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237 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
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238 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
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239 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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240 </when>
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241 </conditional>
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242 <conditional name="contact_options">
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243 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
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244 help="Create a Galaxy workflow to save these values">
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galaxyp
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245 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
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246 <option value="yes">Specify Contact Information</option>
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247 </param>
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248 <when value="no" />
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249 <when value="yes">
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250 <param name="contact_first_name" type="text" value="" label="Contact first name.">
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galaxyp
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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_last_name" type="text" value="" label="Contact last name.">
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254 <validator type="regex" message="">\S+.*</validator>
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255 </param>
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256 <param name="contact_email" type="text" value="" label="Contact e-mail.">
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galaxyp
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257 <validator type="regex" message="">\S+@\S+</validator>
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258 </param>
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259 <param name="contact_address" type="text" value="" label="Contact address.">
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260 <validator type="regex" message="">\S+.*</validator>
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261 </param>
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262 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
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263 </param>
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264 <param name="organization_name" type="text" value="" label="Organization name.">
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265 <validator type="regex" message="">\S+.*</validator>
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266 </param>
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267 <param name="organization_email" type="text" value="" label="Organization e-mail.">
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268 <validator type="regex" message="">\S+@\S+</validator>
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269 </param>
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270 <param name="organization_address" type="text" value="" label="Organization address.">
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271 <validator type="regex" message="">\S+.*</validator>
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272 </param>
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273 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
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274 </param>
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275 </when>
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276 </conditional>
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277
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278 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
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279 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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280 <option value="zip">Zip File for import to Desktop App</option>
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281 <option value="mzidentML" selected="True">mzidentML File</option>
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282 <option value="3">PSM Report</option>
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283 <option value="8">Extended PSM Report</option>
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284 <option value="2">PSM Phosphorylation Report</option>
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285 <option value="5">Peptide Report</option>
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286 <option value="4">Peptide Phosphorylation Report</option>
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287 <option value="7">Protein Report</option>
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288 <option value="6">Protein Phosphorylation Report</option>
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289 <option value="0">Certificate of Analysis</option>
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290 <option value="1">Hierarchical Report</option>
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291 <option value="cps">CPS file</option>
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292 <validator type="no_options" message="Please select at least one output file" />
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293 </param>
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294
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295 </inputs>
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296 <outputs>
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297 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
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298 <filter>'mzidentML' in outputs</filter>
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299 </data>
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300 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
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301 <filter>'cps' in outputs</filter>
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302 </data>
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303 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
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304 <filter>'zip' in outputs</filter>
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305 </data>
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306 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
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307 <filter>'0' in outputs</filter>
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308 </data>
20
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309 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
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310 <filter>'1' in outputs</filter>
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311 </data>
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312 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
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313 <filter>'2' in outputs</filter>
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314 </data>
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315 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
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316 <filter>'3' in outputs</filter>
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317 </data>
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318 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
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galaxyp
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319 <filter>'8' in outputs</filter>
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galaxyp
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320 </data>
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321 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
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322 <filter>'4' in outputs</filter>
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323 </data>
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324 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
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iracooke
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325 <filter>'5' in outputs</filter>
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iracooke
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326 </data>
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327 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
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iracooke
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328 <filter>'6' in outputs</filter>
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329 </data>
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330 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
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331 <filter>'7' in outputs</filter>
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332 </data>
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333 </outputs>
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334 <tests>
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335 <test>
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336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
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337 <param name="processing_options_selector" value="no"/>
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338 <param name="filtering_options_selector" value="no"/>
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galaxyp
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339 <param name="outputs" value="zip,3"/>
33
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galaxyp
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340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
32
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galaxyp
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341 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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342 <assert_contents>
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galaxyp
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343 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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344 </assert_contents>
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galaxyp
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345 </output>
20
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iracooke
parents: 18
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346 </test>
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iracooke
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347 <test>
21
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iracooke
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348 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
20
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iracooke
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349 <param name="processing_options_selector" value="no"/>
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iracooke
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350 <param name="filtering_options_selector" value="yes"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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diff changeset
351 <param name="min_peptide_length" value="1"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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352 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
32
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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353 <output name="output_certificate">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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354 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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355 <has_text text="Tolerance: 100" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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356 <has_text text="Carbamidomethylation of C" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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357 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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358 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
359 <output name="output_hierarchical">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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360 <assert_contents>
33
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galaxyp
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diff changeset
361 <has_text_matching expression="1.1\tcds.comp" />
32
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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362 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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363 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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diff changeset
364 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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365 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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366 <not_has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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367 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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368 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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369 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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diff changeset
370 <output name="output_psm_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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371 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
372 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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373 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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374 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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375 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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diff changeset
376 <output name="output_peptides">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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377 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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378 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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379 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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380 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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381 </output>
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galaxyp
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382 <output name="output_peptides_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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383 <assert_contents>
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galaxyp
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384 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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385 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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386 </assert_contents>
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galaxyp
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387 </output>
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galaxyp
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388 <output name="output_proteins">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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389 <assert_contents>
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galaxyp
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390 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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391 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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392 </assert_contents>
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galaxyp
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393 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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diff changeset
394 <output name="output_proteins_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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395 <assert_contents>
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396 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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397 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
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398 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
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399 </output>
20
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400 </test>
18
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401 </tests>
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402 <help>
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403 **What it does**
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404
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405 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
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406
30
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galaxyp
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diff changeset
407 http://compomics.github.io/projects/peptide-shaker.html
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408 http://compomics.github.io/projects/searchgui.html
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iracooke
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409
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iracooke
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410 ----
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iracooke
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411
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iracooke
parents:
diff changeset
412 Reports
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413 =======
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iracooke
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414
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iracooke
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415
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416 PSM Report
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417 ----------
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418
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419 * Protein(s): Protein(s) to which the peptide can be attached
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iracooke
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420 * Sequence: Sequence of the peptide
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
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421 * Variable Modifications: The variable modifications
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422 * D-score: D-score for variable PTM localization
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423 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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424 * Localization Confidence: The confidence in variable PTM localization.
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425 * Fixed Modifications: The fixed modifications.
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426 * Spectrum File: The spectrum file.
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427 * Spectrum Title: The title of the spectrum.
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428 * Spectrum Scan Number: The spectrum scan number.
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429 * RT: Retention time
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430 * m/z: Measured m/z
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431 * Measured Charge: The charge as given in the spectrum file.
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432 * Identification Charge: The charge as inferred by the search engine.
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433 * Theoretical Mass: The theoretical mass of the peptide.
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434 * Isotope Number: The isotope number targetted by the instrument.
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435 * Precursor m/z Error: The precursor m/z matching error.
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436 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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437 * Confidence: Confidence in percent associated to the retained PSM.
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438 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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439 * Validation: Indicates the validation level of the protein group.
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440
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441
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442 Protein Report
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443 --------------
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444
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445 * Main Accession: Main accession of the protein group.
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446 * Description: Description of the protein designed by the main accession.
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parents:
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447 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
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448 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
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parents:
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449 * PI: Protein Inference status of the protein group.
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parents:
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450 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
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451 * Protein Group: The complete protein group (alphabetical order).
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452 * #Peptides: Total number of peptides.
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453 * #Validated Peptides: Number of validated peptides.
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454 * #Unique: Total number of peptides unique to this protein group.
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parents:
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455 * #PSMs: Number of PSMs
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456 * #Validated PSMs: Number of validated PSMs
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457 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
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parents:
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458 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
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459 * MW (kDa): Molecular Weight.
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parents:
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460 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
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461 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
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462 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
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463 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
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464 * Score: Score of the protein group.
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parents:
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465 * Confidence: Confidence in percent associated to the protein group.
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466 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
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parents:
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467 * Validation: Indicates the validation level of the protein group.
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468
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469
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470 Peptide Report
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471 --------------
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472
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473
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iracooke
parents:
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474 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
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475 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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476 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
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parents:
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477 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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478 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
479 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
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parents:
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480 * Localization Confidence: The confidence in PTMs localization.
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parents:
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481 * Fixed Modifications: The fixed modifications.
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iracooke
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482 * #Validated PSMs: Number of validated PSMs.
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parents:
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483 * #PSMs: Number of PSMs.
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parents:
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484 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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485 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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486 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
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487 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
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488
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489
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490 Hierachical Report
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parents:
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491 ------------------
a5f9b959d5d1 Uploaded
iracooke
parents:
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492
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iracooke
parents:
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493 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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494 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
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495 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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496 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
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497 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
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498 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded
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parents:
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499 * #Validated Peptides: Number of validated peptides.
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parents:
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500 * #Unique: Total number of peptides unique to this protein group.
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parents:
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501 * #PSMs: Number of PSMs
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iracooke
parents:
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502 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded
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parents:
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503 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
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504 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
a5f9b959d5d1 Uploaded
iracooke
parents:
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505 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded
iracooke
parents:
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506 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded
iracooke
parents:
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507 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded
iracooke
parents:
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508 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
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parents:
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509 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded
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parents:
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510 * Score: Score of the protein group.
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parents:
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511 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
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512 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
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513 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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514 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
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515 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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516 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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517 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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518 * Variable Modifications: The variable modifications.
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iracooke
parents:
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519 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
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520 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
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521 * #Validated PSMs: Number of validated PSMs.
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parents:
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522 * #PSMs: Number of PSMs.
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parents:
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523 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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524 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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525 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
526 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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527 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
528 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
529 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
530 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
531 * D-score: D-score for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
532 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
533 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
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534 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
535 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
536 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
537 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
538 * RT: Retention time
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
539 * m/z: Measured m/z
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
540 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
541 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
542 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
543 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
544 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
545 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
546 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
547 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
548 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
549
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iracooke
parents:
diff changeset
550
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iracooke
parents:
diff changeset
551 ------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
552
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parents:
diff changeset
553 **Citation**
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iracooke
parents:
diff changeset
554
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galaxyp
parents: 29
diff changeset
555 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
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iracooke
parents:
diff changeset
556
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
557 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18
a5f9b959d5d1 Uploaded
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parents:
diff changeset
558 </help>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
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diff changeset
559 <expand macro="citations" />
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iracooke
parents:
diff changeset
560 </tool>