Mercurial > repos > jjohnson > peptideshaker

annotate peptide_shaker.xml @ 1:fa76abf69433 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
author jjohnson
date Fri, 08 Jun 2018 15:58:53 -0400
parents 8b99cb00e1c4
children eea7e945f479
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fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
jjohnson
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.23.0">
0
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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_basic.xml</import>
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7 </macros>
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8 <requirements>
1
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9 <requirement type="package" version="1.16.23">peptide-shaker</requirement>
0
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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 $bin_dir = "bin"
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19
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20
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21 mkdir output_reports;
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22 cwd=`pwd`;
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23
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24 ln -s '$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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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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39 #set $cleaned_list = str($outputs).split(',')
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40 #if 'cps' in $cleaned_list:
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41 #silent $cleaned_list.remove('cps')
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42 #end if
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43 #if 'mzidentML' in $cleaned_list:
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44 #silent $cleaned_list.remove('mzidentML')
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45 #end if
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46 #if 'zip' in $cleaned_list:
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47 #silent $cleaned_list.remove('zip')
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48 #end if
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49 #if len($cleaned_list) > 0
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50 ## Only numbers are left over. These corresponds to different reports.
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51 -reports #echo ','.join($cleaned_list)#
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52 #end if
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53
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54 -threads "\${GALAXY_SLOTS:-12}"
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55
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57
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58 2>> $temp_stderr)
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59
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60 &&
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61
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62 echo "Running Reports";
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63
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64 ##################################
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65 ## PeptideShaker Report options ##
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66 ##################################
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67
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68 #if 'mzidentML' in str($outputs).split(','):
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69 echo "Generating mzIdentML";
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70 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
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71 --exec_dir="\$cwd/${bin_dir}"
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72 -in \$cwd/peptideshaker_output.zip
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73 -output_file \$cwd/output.mzid
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74 #if $contact_options.contact_options_selector == "yes":
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75 -contact_first_name "$contact_options.contact_first_name"
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76 -contact_last_name "$contact_options.contact_last_name"
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77 -contact_email "$contact_options.contact_email"
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78 -contact_address "$contact_options.contact_address"
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79 #if str($contact_options.contact_url).strip() != '':
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80 -contact_url = "$contact_options.contact_url"
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81 #end if
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82 -organization_name "$contact_options.organization_name"
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83 -organization_email "$contact_options.organization_email"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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84 -organization_address "$contact_options.organization_address"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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85 #if str($contact_options.organization_url).strip() != '':
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86 -organization_url = "$contact_options.organization_url"
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87 #end if
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88 #else:
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89 -contact_first_name "Proteomics"
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90 -contact_last_name "Galaxy"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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91 -contact_email "galaxyp@umn.edu"
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92 -contact_address "galaxyp@umn.edu"
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93 -organization_name "University of Minnesota"
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94 -organization_email "galaxyp@umn.edu"
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95 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
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96 #end if
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97 2>> $temp_stderr)
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98 &&
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99 #end if
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100
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101 ## Generate Reports if the user has selected one of the 8 additional reports
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102 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
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103 ## and will not be passed to the command line
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104 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
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105
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106 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
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107 --exec_dir="\$cwd/${bin_dir}"
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108 -temp_folder \$cwd/ReportCLI
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109 -in \$cwd/peptideshaker_output.zip
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110 -out_reports \$cwd/output_reports
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111 #set $cleaned_list = str($outputs).split(',')
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112 #if 'cps' in $cleaned_list:
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113 #silent $cleaned_list.remove('cps')
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114 #end if
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115 #if 'mzidentML' in $cleaned_list:
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116 #silent $cleaned_list.remove('mzidentML')
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117 #end if
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118 #if 'zip' in $cleaned_list:
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119 #silent $cleaned_list.remove('zip')
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120 #end if
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121 ## Only numbers are left over. These corresponds to different reports.
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122 -reports #echo ','.join($cleaned_list)#
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123
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124 2>> $temp_stderr)
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125 &&
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126 #end if
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127
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128 ## # ls -l \$cwd/output_reports/* ;
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129
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130 #if '0' in str($outputs).split(','):
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131 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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132 ;
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133 #end if
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134 #if '1' in str($outputs).split(','):
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135 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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136 ;
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137 #end if
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138 #if '2' in str($outputs).split(','):
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139 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
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140 ;
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141 #end if
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142 #if '8' in str($outputs).split(','):
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143 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
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144 ;
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145 #end if
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146 #if '3' in str($outputs).split(','):
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147 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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148 ;
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149 #end if
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150 #if '4' in str($outputs).split(','):
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151 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
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152 ;
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153 #end if
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154 #if '5' in str($outputs).split(','):
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155 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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156 ;
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157 #end if
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158 #if '6' in str($outputs).split(','):
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159 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
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160 ;
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161 #end if
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162 #if '7' in str($outputs).split(','):
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163 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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164 ;
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165 #end if
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166
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167 exit_code_for_galaxy=\$?;
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168 cat $temp_stderr 2>&1;
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169 (exit \$exit_code_for_galaxy)
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170
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171 ]]>
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172 </command>
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173 <inputs>
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174 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
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175 help="SearchGUI Results from History">
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176 <options options_filter_attribute="metadata.searchgui_major_version" >
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177 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
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178 </options>
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179 </param>
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180
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181
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182 <conditional name="contact_options">
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183 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
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184 help="Create a Galaxy workflow to save these values">
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185 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
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186 <option value="yes">Specify Contact Information</option>
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187 </param>
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188 <when value="no" />
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189 <when value="yes">
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190 <param name="contact_first_name" type="text" value="" label="Contact first name.">
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191 <validator type="regex" message="">\S+.*</validator>
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192 </param>
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193 <param name="contact_last_name" type="text" value="" label="Contact last name.">
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194 <validator type="regex" message="">\S+.*</validator>
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195 </param>
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196 <param name="contact_email" type="text" value="" label="Contact e-mail.">
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197 <validator type="regex" message="">\S+@\S+</validator>
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198 </param>
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199 <param name="contact_address" type="text" value="" label="Contact address.">
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200 <validator type="regex" message="">\S+.*</validator>
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201 </param>
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202 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
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203 </param>
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204 <param name="organization_name" type="text" value="" label="Organization name.">
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205 <validator type="regex" message="">\S+.*</validator>
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206 </param>
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207 <param name="organization_email" type="text" value="" label="Organization e-mail.">
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208 <validator type="regex" message="">\S+@\S+</validator>
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209 </param>
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210 <param name="organization_address" type="text" value="" label="Organization address.">
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211 <validator type="regex" message="">\S+.*</validator>
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212 </param>
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213 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
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214 </param>
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215 </when>
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216 </conditional>
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217
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218 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
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219 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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220 <option value="zip">Zip File for import to Desktop App</option>
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221 <option value="mzidentML" selected="True">mzidentML File</option>
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222 <option value="3">PSM Report</option>
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223 <option value="8">Extended PSM Report</option>
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224 <option value="2">PSM Phosphorylation Report</option>
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225 <option value="5">Peptide Report</option>
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226 <option value="4">Peptide Phosphorylation Report</option>
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227 <option value="7">Protein Report</option>
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228 <option value="6">Protein Phosphorylation Report</option>
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229 <option value="0">Certificate of Analysis</option>
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230 <option value="1">Hierarchical Report</option>
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231 <option value="cps">CPS file</option>
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232 <validator type="no_options" message="Please select at least one output file" />
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233 </param>
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234
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235 </inputs>
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236 <outputs>
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237 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
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238 <filter>'mzidentML' in outputs</filter>
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239 </data>
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240 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
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241 <filter>'cps' in outputs</filter>
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242 </data>
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243 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
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244 <filter>'zip' in outputs</filter>
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245 </data>
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246 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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247 <filter>'0' in outputs</filter>
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248 </data>
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249 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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250 <filter>'1' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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251 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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252 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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253 <filter>'2' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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254 </data>
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255 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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256 <filter>'3' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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257 </data>
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258 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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259 <filter>'8' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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260 </data>
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261 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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262 <filter>'4' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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263 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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264 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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265 <filter>'5' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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266 </data>
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267 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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268 <filter>'6' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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269 </data>
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270 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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271 <filter>'7' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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272 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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273 </outputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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274 <tests>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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275 <test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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276 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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277 <param name="processing_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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278 <param name="filtering_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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279 <param name="outputs" value="zip,3"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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280 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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281 <output name="output_psm">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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282 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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283 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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284 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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285 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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286 </test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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287 <test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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288 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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289 <param name="processing_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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290 <param name="filtering_options_selector" value="yes"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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291 <param name="min_peptide_length" value="1"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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292 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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293 <output name="output_certificate">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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294 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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295 <has_text text="Tolerance: 100" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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296 <has_text text="Carbamidomethylation of C" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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297 </assert_contents>
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298 </output>
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299 <output name="output_hierarchical">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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300 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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301 <has_text_matching expression="1.1\tcds.comp" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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302 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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303 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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304 <output name="output_psm">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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305 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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306 <not_has_text text="Phosphosite" />
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307 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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308 </assert_contents>
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309 </output>
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310 <output name="output_psm_phosphorylation">
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311 <assert_contents>
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312 <has_text text="Phosphosite" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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313 <has_text text="cds.comp41779_c0_seq1" />
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314 </assert_contents>
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315 </output>
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316 <output name="output_peptides">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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317 <assert_contents>
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318 <has_text text="Modification" />
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319 <has_text text="cds.comp41779_c0_seq1" />
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320 </assert_contents>
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321 </output>
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322 <output name="output_peptides_phosphorylation">
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323 <assert_contents>
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324 <has_text text="Phosphosite" />
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325 <has_text text="cds.comp41779_c0_seq1" />
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326 </assert_contents>
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327 </output>
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328 <output name="output_proteins">
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329 <assert_contents>
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330 <has_text text="Modification" />
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331 <has_text text="cds.comp41779_c0_seq1" />
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332 </assert_contents>
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333 </output>
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334 <output name="output_proteins_phosphorylation">
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335 <assert_contents>
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336 <has_text text="Phosphosite" />
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337 <has_text text="cds.comp41779_c0_seq1" />
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338 </assert_contents>
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339 </output>
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340 </test>
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341 <test>
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342 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
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343 <param name="processing_options_selector" value="no"/>
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344 <param name="filtering_options_selector" value="no"/>
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345 <param name="outputs" value="3,cps"/>
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346 <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
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347 <output name="output_psm">
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348 <assert_contents>
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349 <has_text text="cds.comp41779_c0_seq1" />
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350 </assert_contents>
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351 </output>
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352 </test>
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353 </tests>
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354 <help>
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355 **What it does**
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356
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357 Combines search results given by SearchGUI after running multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists.
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358
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359 http://compomics.github.io/projects/peptide-shaker.html
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360
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361 http://compomics.github.io/projects/searchgui.html
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362
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363 ----
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364
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365 Reports
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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366 =======
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367
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368
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369 PSM Report
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370 ----------
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371
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372 * Protein(s): Protein(s) to which the peptide can be attached
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373 * Sequence: Sequence of the peptide
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374 * Variable Modifications: The variable modifications
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375 * D-score: D-score for variable PTM localization
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376 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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377 * Localization Confidence: The confidence in variable PTM localization.
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378 * Fixed Modifications: The fixed modifications.
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379 * Spectrum File: The spectrum file.
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380 * Spectrum Title: The title of the spectrum.
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381 * Spectrum Scan Number: The spectrum scan number.
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382 * RT: Retention time
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383 * m/z: Measured m/z
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384 * Measured Charge: The charge as given in the spectrum file.
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385 * Identification Charge: The charge as inferred by the search engine.
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386 * Theoretical Mass: The theoretical mass of the peptide.
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387 * Isotope Number: The isotope number targetted by the instrument.
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388 * Precursor m/z Error: The precursor m/z matching error.
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389 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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390 * Confidence: Confidence in percent associated to the retained PSM.
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391 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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392 * Validation: Indicates the validation level of the protein group.
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393
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394
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395 Protein Report
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396 --------------
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397
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398 * Main Accession: Main accession of the protein group.
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399 * Description: Description of the protein designed by the main accession.
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400 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
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401 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
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402 * PI: Protein Inference status of the protein group.
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403 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
404 * Protein Group: The complete protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
405 * #Peptides: Total number of peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
406 * #Validated Peptides: Number of validated peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
407 * #Unique: Total number of peptides unique to this protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
408 * #PSMs: Number of PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
409 * #Validated PSMs: Number of validated PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
410 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
411 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
412 * MW (kDa): Molecular Weight.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
413 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
414 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
415 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
416 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
417 * Score: Score of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
418 * Confidence: Confidence in percent associated to the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
419 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
420 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
421
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
422
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
423 Peptide Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
424 --------------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
425
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
426
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
427 * Protein(s): Protein(s) to which this peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
428 * AAs Before: The amino-acids before the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
429 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
430 * AAs After: The amino-acids after the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
431 * Modified Sequence: The peptide sequence annotated with variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
432 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
433 * Localization Confidence: The confidence in PTMs localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
434 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
435 * #Validated PSMs: Number of validated PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
436 * #PSMs: Number of PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
437 * Score: Score of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
438 * Confidence: Confidence in percent associated to the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
439 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
440 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
441
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
442
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
443 Hierachical Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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444 ------------------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
445
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
446 * Main Accession: Main accession of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
447 * Description: Description of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
448 * PI: Protein Inference status of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
449 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
450 * Protein Group: The complete protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
451 * #Peptides: Total number of peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
452 * #Validated Peptides: Number of validated peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
453 * #Unique: Total number of peptides unique to this protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
454 * #PSMs: Number of PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
455 * #Validated PSMs: Number of validated PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
456 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
457 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
458 * MW (kDa): Molecular Weight.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
459 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
460 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
461 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
462 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
463 * Score: Score of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
464 * Confidence: Confidence in percent associated to the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
465 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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466 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
467 * Protein(s): Protein(s) to which this peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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468 * AAs Before: The amino-acids before the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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469 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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470 * AAs After: The amino-acids after the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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471 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
472 * Localization Confidence: The confidence in PTMs localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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473 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
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474 * #Validated PSMs: Number of validated PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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475 * #PSMs: Number of PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
476 * Score: Score of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
477 * Confidence: Confidence in percent associated to the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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478 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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479 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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480 * Protein(s): Protein(s) to which the peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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481 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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482 * Modified Sequence: The peptide sequence annotated with variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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483 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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484 * D-score: D-score for variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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485 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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486 * Localization Confidence: The confidence in variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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487 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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488 * Spectrum File: The spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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489 * Spectrum Title: The title of the spectrum.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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490 * Spectrum Scan Number: The spectrum scan number.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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491 * RT: Retention time
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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492 * m/z: Measured m/z
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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493 * Measured Charge: The charge as given in the spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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494 * Identification Charge: The charge as inferred by the search engine.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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495 * Theoretical Mass: The theoretical mass of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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496 * Isotope Number: The isotope number targetted by the instrument.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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497 * Precursor m/z Error: The precursor m/z matching error.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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498 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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499 * Confidence: Confidence in percent associated to the retained PSM.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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500 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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501 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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502
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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503
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jjohnson
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504 ------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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505
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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506 **Citation**
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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507
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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508 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
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509
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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510 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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511 </help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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512 <expand macro="citations" />
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513 </tool>