Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 46:baeced706dbc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
author galaxyp
date Wed, 11 Jul 2018 08:14:23 -0400
parents 5fa8b409599e
children 58a3e6cb2598
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46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26">
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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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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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9 <requirement type="package" version="1.16.26">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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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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54 -threads "\${GALAXY_SLOTS:-12}"
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56 ##Optional processing parameters:
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57 #if $processing_options.processing_options_selector == "yes"
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58 -protein_fdr "${processing_options.protein_fdr}"
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59 -peptide_fdr "${processing_options.peptide_fdr}"
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60 -psm_fdr "${processing_options.psm_fdr}"
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61 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
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62 #if $processing_options.ptm_score.ptm_score_selector == 1
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63 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
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64 #if str($processing_options.ptm_score.ptm_threshold) != ''
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65 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
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66 #end if
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67 #end if
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68 -ptm_alignment "${processing_options.ptm_alignment}"
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69 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
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70 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
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71 #end if
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72
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73 ##Optional filtering parameters:
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74 #if $filtering_options.filtering_options_selector == "yes":
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75 -import_peptide_length_min "${filtering_options.min_peptide_length}"
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76 -import_peptide_length_max "${filtering_options.max_peptide_length}"
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77 -import_precurosor_mz "${filtering_options.max_precursor_error}"
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78 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
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79 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
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80 ##-max_omssa_e "${filtering_options.max_omssa_e}"
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81 ##-max_mascot_e "${filtering_options.max_mascot_e}"
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82 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
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83 #end if
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84
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85 2>> $temp_stderr)
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87 &&
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89 echo "Running Reports";
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91 ##################################
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92 ## PeptideShaker Report options ##
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93 ##################################
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94
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95 #if 'mzidentML' in str($outputs).split(','):
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96 echo "Generating mzIdentML";
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97 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
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98 --exec_dir="\$cwd/${bin_dir}"
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99 -in \$cwd/peptideshaker_output.zip
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100 -output_file \$cwd/output.mzid
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101 #if $contact_options.contact_options_selector == "yes":
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102 -contact_first_name "$contact_options.contact_first_name"
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103 -contact_last_name "$contact_options.contact_last_name"
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104 -contact_email "$contact_options.contact_email"
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galaxyp
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105 -contact_address "$contact_options.contact_address"
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galaxyp
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106 #if str($contact_options.contact_url).strip() != '':
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galaxyp
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107 -contact_url = "$contact_options.contact_url"
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galaxyp
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108 #end if
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galaxyp
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109 -organization_name "$contact_options.organization_name"
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galaxyp
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110 -organization_email "$contact_options.organization_email"
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galaxyp
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111 -organization_address "$contact_options.organization_address"
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galaxyp
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112 #if str($contact_options.organization_url).strip() != '':
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113 -organization_url = "$contact_options.organization_url"
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galaxyp
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114 #end if
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galaxyp
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115 #else:
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galaxyp
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116 -contact_first_name "Proteomics"
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galaxyp
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117 -contact_last_name "Galaxy"
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galaxyp
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118 -contact_email "galaxyp@umn.edu"
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galaxyp
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119 -contact_address "galaxyp@umn.edu"
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galaxyp
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120 -organization_name "University of Minnesota"
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galaxyp
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121 -organization_email "galaxyp@umn.edu"
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galaxyp
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122 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
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galaxyp
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123 #end if
44
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124 2>> $temp_stderr)
20
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125 &&
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126 #end if
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127
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128 ## Generate Reports if the user has selected one of the 8 additional reports
44
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129 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
20
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130 ## and will not be passed to the command line
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131 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
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132
30
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133 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
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134 --exec_dir="\$cwd/${bin_dir}"
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135 -temp_folder \$cwd/ReportCLI
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136 -in \$cwd/peptideshaker_output.zip
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137 -out_reports \$cwd/output_reports
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138 #set $cleaned_list = str($outputs).split(',')
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139 #if 'cps' in $cleaned_list:
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140 #silent $cleaned_list.remove('cps')
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141 #end if
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142 #if 'mzidentML' in $cleaned_list:
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143 #silent $cleaned_list.remove('mzidentML')
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144 #end if
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145 #if 'zip' in $cleaned_list:
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146 #silent $cleaned_list.remove('zip')
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iracooke
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147 #end if
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148 ## Only numbers are left over. These corresponds to different reports.
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149 -reports #echo ','.join($cleaned_list)#
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150
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151 2>> $temp_stderr)
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152 &&
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153 #end if
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154
30
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155 ## # ls -l \$cwd/output_reports/* ;
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156
18
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157 #if '0' in str($outputs).split(','):
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158 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
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159 ;
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160 #end if
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161 #if '1' in str($outputs).split(','):
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162 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
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163 ;
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164 #end if
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165 #if '2' in str($outputs).split(','):
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166 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
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167 ;
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168 #end if
30
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169 #if '8' in str($outputs).split(','):
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170 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
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171 ;
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172 #end if
20
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173 #if '3' in str($outputs).split(','):
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174 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
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175 ;
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176 #end if
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177 #if '4' in str($outputs).split(','):
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178 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
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179 ;
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180 #end if
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181 #if '5' in str($outputs).split(','):
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182 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
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183 ;
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184 #end if
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185 #if '6' in str($outputs).split(','):
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186 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
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187 ;
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188 #end if
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189 #if '7' in str($outputs).split(','):
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190 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
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191 ;
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192 #end if
18
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193
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194 exit_code_for_galaxy=\$?;
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195 cat $temp_stderr 2>&1;
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196 (exit \$exit_code_for_galaxy)
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197
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198 ]]>
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199 </command>
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200 <inputs>
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201 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
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202 help="SearchGUI Results from History">
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203 <options options_filter_attribute="metadata.searchgui_major_version" >
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204 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
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205 </options>
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206 </param>
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207 <conditional name="processing_options">
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208 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
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209 <option value="no" selected="True">Default Processing Options</option>
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210 <option value="yes">Advanced Processing Options</option>
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211 </param>
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212 <when value="no" />
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213 <when value="yes">
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214 <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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215 <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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216 <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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217 <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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218 help="default 95%: '95.0'" />
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219 <conditional name="ptm_score">
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220 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
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221 <option value="0" selected="True">A-score</option>
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222 <option value="1">PhosphoRS</option>
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223 <option value="2">None</option>
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224 </param>
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225 <when value="0" />
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226 <when value="1">
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227 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
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228 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
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229 help="Automatic mode will be used if not set" />
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230 </when>
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231 <when value="2" />
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232 </conditional>
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233 <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
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234 <option value="0">Character Sequence</option>
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235 <option value="1" selected="true">Amino Acids</option>
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236 <option value="2">Indistinguishable Amino Acids</option>
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237 </param>
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238 <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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239 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
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240 </when>
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241 </conditional>
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242 <conditional name="filtering_options">
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243 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
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244 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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245 <option value="no" selected="True">Default Filtering Options</option>
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246 <option value="yes">Advanced Filtering Options</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="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
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251 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
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252 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
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253 help="Next option specifies units (Da or ppm)" />
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254 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
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255 <option value="1">ppm</option>
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256 <option value="0">Daltons</option>
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257 </param>
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258 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
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259 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
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260 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
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261 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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262 </when>
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263 </conditional>
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264 <conditional name="contact_options">
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265 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
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266 help="Create a Galaxy workflow to save these values">
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267 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
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268 <option value="yes">Specify Contact Information</option>
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269 </param>
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270 <when value="no" />
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271 <when value="yes">
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272 <param name="contact_first_name" type="text" value="" label="Contact first name.">
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273 <validator type="regex" message="">\S+.*</validator>
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274 </param>
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275 <param name="contact_last_name" type="text" value="" label="Contact last name.">
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276 <validator type="regex" message="">\S+.*</validator>
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277 </param>
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278 <param name="contact_email" type="text" value="" label="Contact e-mail.">
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279 <validator type="regex" message="">\S+@\S+</validator>
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280 </param>
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281 <param name="contact_address" type="text" value="" label="Contact address.">
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282 <validator type="regex" message="">\S+.*</validator>
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283 </param>
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284 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
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285 </param>
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286 <param name="organization_name" type="text" value="" label="Organization name.">
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287 <validator type="regex" message="">\S+.*</validator>
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288 </param>
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289 <param name="organization_email" type="text" value="" label="Organization e-mail.">
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290 <validator type="regex" message="">\S+@\S+</validator>
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291 </param>
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292 <param name="organization_address" type="text" value="" label="Organization address.">
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293 <validator type="regex" message="">\S+.*</validator>
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294 </param>
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295 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
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296 </param>
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297 </when>
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298 </conditional>
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299
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300 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
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301 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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302 <option value="zip">Zip File for import to Desktop App</option>
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303 <option value="mzidentML" selected="True">mzidentML File</option>
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304 <option value="3">PSM Report</option>
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305 <option value="8">Extended PSM Report</option>
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306 <option value="2">PSM Phosphorylation Report</option>
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307 <option value="5">Peptide Report</option>
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308 <option value="4">Peptide Phosphorylation Report</option>
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309 <option value="7">Protein Report</option>
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310 <option value="6">Protein Phosphorylation Report</option>
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311 <option value="0">Certificate of Analysis</option>
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312 <option value="1">Hierarchical Report</option>
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313 <option value="cps">CPS file</option>
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314 <validator type="no_options" message="Please select at least one output file" />
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315 </param>
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316
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317 </inputs>
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318 <outputs>
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319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
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320 <filter>'mzidentML' in outputs</filter>
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321 </data>
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322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
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323 <filter>'cps' in outputs</filter>
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324 </data>
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325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
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326 <filter>'zip' in outputs</filter>
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327 </data>
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328 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
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329 <filter>'0' in outputs</filter>
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330 </data>
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331 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
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332 <filter>'1' in outputs</filter>
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333 </data>
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334 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
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335 <filter>'2' in outputs</filter>
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336 </data>
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337 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
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338 <filter>'3' in outputs</filter>
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339 </data>
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340 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
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galaxyp
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341 <filter>'8' in outputs</filter>
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342 </data>
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343 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
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344 <filter>'4' in outputs</filter>
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345 </data>
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346 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
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iracooke
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347 <filter>'5' in outputs</filter>
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348 </data>
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349 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
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iracooke
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350 <filter>'6' in outputs</filter>
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351 </data>
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352 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
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353 <filter>'7' in outputs</filter>
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354 </data>
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355 </outputs>
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356 <tests>
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357 <test>
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358 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
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359 <param name="processing_options_selector" value="no"/>
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360 <param name="filtering_options_selector" value="no"/>
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361 <param name="outputs" value="zip,3"/>
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362 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
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galaxyp
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363 <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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364 <assert_contents>
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galaxyp
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365 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
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366 </assert_contents>
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367 </output>
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iracooke
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368 </test>
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369 <test>
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diff changeset
370 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
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iracooke
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371 <param name="processing_options_selector" value="no"/>
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372 <param name="filtering_options_selector" value="yes"/>
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iracooke
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373 <param name="min_peptide_length" value="1"/>
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iracooke
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374 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
32
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galaxyp
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375 <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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376 <assert_contents>
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galaxyp
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377 <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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378 <has_text text="Carbamidomethylation of C" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
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379 </assert_contents>
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380 </output>
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galaxyp
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diff changeset
381 <output name="output_hierarchical">
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382 <assert_contents>
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galaxyp
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383 <has_text_matching expression="1.1\tcds.comp" />
32
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384 </assert_contents>
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385 </output>
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galaxyp
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diff changeset
386 <output name="output_psm">
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galaxyp
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387 <assert_contents>
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galaxyp
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388 <not_has_text text="Phosphosite" />
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galaxyp
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389 <has_text text="cds.comp41779_c0_seq1" />
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390 </assert_contents>
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391 </output>
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galaxyp
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diff changeset
392 <output name="output_psm_phosphorylation">
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galaxyp
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393 <assert_contents>
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galaxyp
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394 <has_text text="Phosphosite" />
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galaxyp
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395 <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
parents: 30
diff changeset
396 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
397 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
398 <output name="output_peptides">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
399 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
400 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
401 <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
parents: 30
diff changeset
402 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
403 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
404 <output name="output_peptides_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
405 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
406 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
407 <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
parents: 30
diff changeset
408 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
409 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
410 <output name="output_proteins">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
411 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
412 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
413 <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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414 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
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415 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
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416 <output name="output_proteins_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
417 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
418 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
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419 <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
parents: 30
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420 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
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421 </output>
20
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iracooke
parents: 18
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422 </test>
44
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galaxyp
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423 <test>
46
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galaxyp
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diff changeset
424 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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425 <param name="processing_options_selector" value="no"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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diff changeset
426 <param name="filtering_options_selector" value="no"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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427 <param name="outputs" value="3,cps"/>
46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
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428 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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429 <output name="output_psm">
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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diff changeset
430 <assert_contents>
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galaxyp
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diff changeset
431 <has_text text="cds.comp41779_c0_seq1" />
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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diff changeset
432 </assert_contents>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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diff changeset
433 </output>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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434 </test>
18
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iracooke
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435 </tests>
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436 <help>
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437 **What it does**
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438
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439 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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iracooke
parents:
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440
30
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galaxyp
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diff changeset
441 http://compomics.github.io/projects/peptide-shaker.html
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
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442 http://compomics.github.io/projects/searchgui.html
18
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iracooke
parents:
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443
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iracooke
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444 ----
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iracooke
parents:
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445
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iracooke
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446 Reports
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447 =======
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parents:
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448
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449
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iracooke
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450 PSM Report
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parents:
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451 ----------
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iracooke
parents:
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452
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iracooke
parents:
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453 * Protein(s): Protein(s) to which the peptide can be attached
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
454 * Sequence: Sequence of the peptide
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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455 * Variable Modifications: The variable modifications
18
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iracooke
parents:
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456 * D-score: D-score for variable PTM localization
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iracooke
parents:
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457 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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iracooke
parents:
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458 * Localization Confidence: The confidence in variable PTM localization.
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iracooke
parents:
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459 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
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460 * Spectrum File: The spectrum file.
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iracooke
parents:
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461 * Spectrum Title: The title of the spectrum.
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iracooke
parents:
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462 * Spectrum Scan Number: The spectrum scan number.
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iracooke
parents:
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463 * RT: Retention time
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iracooke
parents:
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464 * m/z: Measured m/z
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parents:
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465 * Measured Charge: The charge as given in the spectrum file.
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parents:
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466 * Identification Charge: The charge as inferred by the search engine.
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parents:
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467 * Theoretical Mass: The theoretical mass of the peptide.
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iracooke
parents:
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468 * Isotope Number: The isotope number targetted by the instrument.
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469 * Precursor m/z Error: The precursor m/z matching error.
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iracooke
parents:
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470 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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parents:
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471 * Confidence: Confidence in percent associated to the retained PSM.
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iracooke
parents:
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472 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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iracooke
parents:
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473 * Validation: Indicates the validation level of the protein group.
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parents:
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474
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475
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iracooke
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476 Protein Report
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477 --------------
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parents:
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478
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parents:
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479 * Main Accession: Main accession of the protein group.
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iracooke
parents:
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480 * Description: Description of the protein designed by the main accession.
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iracooke
parents:
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481 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
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iracooke
parents:
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482 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
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iracooke
parents:
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483 * PI: Protein Inference status of the protein group.
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iracooke
parents:
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484 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
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iracooke
parents:
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485 * Protein Group: The complete protein group (alphabetical order).
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iracooke
parents:
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486 * #Peptides: Total number of peptides.
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iracooke
parents:
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487 * #Validated Peptides: Number of validated peptides.
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iracooke
parents:
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488 * #Unique: Total number of peptides unique to this protein group.
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parents:
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489 * #PSMs: Number of PSMs
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iracooke
parents:
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490 * #Validated PSMs: Number of validated PSMs
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iracooke
parents:
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491 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
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iracooke
parents:
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492 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
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iracooke
parents:
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493 * MW (kDa): Molecular Weight.
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parents:
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494 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
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iracooke
parents:
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495 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
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iracooke
parents:
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496 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
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497 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
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iracooke
parents:
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498 * Score: Score of the protein group.
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iracooke
parents:
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499 * Confidence: Confidence in percent associated to the protein group.
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iracooke
parents:
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500 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
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iracooke
parents:
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501 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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502
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iracooke
parents:
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503
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parents:
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504 Peptide Report
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iracooke
parents:
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505 --------------
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parents:
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506
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
507
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parents:
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508 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
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509 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
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510 * Sequence: Sequence of the peptide.
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iracooke
parents:
diff changeset
511 * AAs After: The amino-acids after the sequence.
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iracooke
parents:
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512 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
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513 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
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514 * Localization Confidence: The confidence in PTMs localization.
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iracooke
parents:
diff changeset
515 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
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516 * #Validated PSMs: Number of validated PSMs.
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iracooke
parents:
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517 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
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518 * Score: Score of the peptide.
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iracooke
parents:
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519 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
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520 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
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521 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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522
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iracooke
parents:
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523
a5f9b959d5d1 Uploaded
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524 Hierachical Report
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iracooke
parents:
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525 ------------------
a5f9b959d5d1 Uploaded
iracooke
parents:
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526
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iracooke
parents:
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527 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
528 * Description: Description of the protein designed by the main accession.
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iracooke
parents:
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529 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
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530 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
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iracooke
parents:
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531 * Protein Group: The complete protein group (alphabetical order).
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iracooke
parents:
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532 * #Peptides: Total number of peptides.
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533 * #Validated Peptides: Number of validated peptides.
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iracooke
parents:
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534 * #Unique: Total number of peptides unique to this protein group.
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iracooke
parents:
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535 * #PSMs: Number of PSMs
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iracooke
parents:
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536 * #Validated PSMs: Number of validated PSMs
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iracooke
parents:
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537 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
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iracooke
parents:
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538 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
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iracooke
parents:
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539 * MW (kDa): Molecular Weight.
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iracooke
parents:
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540 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
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iracooke
parents:
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541 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
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iracooke
parents:
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542 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
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iracooke
parents:
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543 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
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iracooke
parents:
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544 * Score: Score of the protein group.
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iracooke
parents:
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545 * Confidence: Confidence in percent associated to the protein group.
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iracooke
parents:
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546 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
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iracooke
parents:
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547 * Validation: Indicates the validation level of the protein group.
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iracooke
parents:
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548 * Protein(s): Protein(s) to which this peptide can be attached.
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iracooke
parents:
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549 * AAs Before: The amino-acids before the sequence.
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iracooke
parents:
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550 * Sequence: Sequence of the peptide.
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iracooke
parents:
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551 * AAs After: The amino-acids after the sequence.
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iracooke
parents:
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552 * Variable Modifications: The variable modifications.
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iracooke
parents:
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553 * Localization Confidence: The confidence in PTMs localization.
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iracooke
parents:
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554 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
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555 * #Validated PSMs: Number of validated PSMs.
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iracooke
parents:
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556 * #PSMs: Number of PSMs.
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iracooke
parents:
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557 * Score: Score of the peptide.
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iracooke
parents:
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558 * Confidence: Confidence in percent associated to the peptide.
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iracooke
parents:
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559 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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iracooke
parents:
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560 * Validation: Indicates the validation level of the protein group.
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iracooke
parents:
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561 * Protein(s): Protein(s) to which the peptide can be attached.
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iracooke
parents:
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562 * Sequence: Sequence of the peptide.
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iracooke
parents:
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563 * Modified Sequence: The peptide sequence annotated with variable modifications.
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iracooke
parents:
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564 * Variable Modifications: The variable modifications.
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iracooke
parents:
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565 * D-score: D-score for variable PTM localization.
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iracooke
parents:
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566 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
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iracooke
parents:
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567 * Localization Confidence: The confidence in variable PTM localization.
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iracooke
parents:
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568 * Fixed Modifications: The fixed modifications.
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iracooke
parents:
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569 * Spectrum File: The spectrum file.
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iracooke
parents:
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570 * Spectrum Title: The title of the spectrum.
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iracooke
parents:
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571 * Spectrum Scan Number: The spectrum scan number.
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iracooke
parents:
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572 * RT: Retention time
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iracooke
parents:
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573 * m/z: Measured m/z
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iracooke
parents:
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574 * Measured Charge: The charge as given in the spectrum file.
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iracooke
parents:
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575 * Identification Charge: The charge as inferred by the search engine.
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iracooke
parents:
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576 * Theoretical Mass: The theoretical mass of the peptide.
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iracooke
parents:
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577 * Isotope Number: The isotope number targetted by the instrument.
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iracooke
parents:
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578 * Precursor m/z Error: The precursor m/z matching error.
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iracooke
parents:
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579 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
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iracooke
parents:
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580 * Confidence: Confidence in percent associated to the retained PSM.
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iracooke
parents:
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581 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
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iracooke
parents:
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582 * Validation: Indicates the validation level of the protein group.
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iracooke
parents:
diff changeset
583
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iracooke
parents:
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584
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iracooke
parents:
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585 ------
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iracooke
parents:
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586
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iracooke
parents:
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587 **Citation**
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iracooke
parents:
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588
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ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
589 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:
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590
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
591 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18
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iracooke
parents:
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592 </help>
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2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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diff changeset
593 <expand macro="citations" />
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iracooke
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594 </tool>