Mercurial > repos > galaxyp > peptideshaker
annotate peptide_shaker.xml @ 18:ffed32e397cb draft
Uploaded
author | galaxyp |
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date | Wed, 11 Jan 2017 13:06:06 -0500 |
parents | 2f8e9d0351a8 |
children | ef4ac2d49ff0 |
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18 | 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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2 <description> |
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3 Perform protein identification using various search engines based on results from SearchGUI |
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4 </description> |
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5 <macros> |
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6 <import>macros.xml</import> |
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7 </macros> |
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8 <requirements> |
18 | 9 <requirement type="package" version="1.13.6">peptide-shaker</requirement> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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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" |
18 | 18 #set $bin_dir = "bin" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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19 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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20 |
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21 mkdir output_reports; |
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22 cwd=`pwd`; |
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23 |
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24 ln -s '$searchgui_input' searchgui_input.zip && |
18 | 25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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26 ###################### |
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27 ## PeptideShakerCLI ## |
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28 ###################### |
18 | 29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI |
30 --exec_dir="\$cwd/${bin_dir}" | |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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31 -temp_folder \$cwd/PeptideShakerCLI |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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32 -experiment '$exp_str' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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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 |
18 | 36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par |
15 | 37 -out \$cwd/peptideshaker_output.cpsx |
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38 -zip \$cwd/peptideshaker_output.zip |
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39 |
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40 -threads "\${GALAXY_SLOTS:-12}" |
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41 |
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42 ##Optional processing parameters: |
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43 #if $processing_options.processing_options_selector == "yes" |
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44 -protein_fdr "${processing_options.protein_fdr}" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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45 -peptide_fdr "${processing_options.peptide_fdr}" |
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46 -psm_fdr "${processing_options.psm_fdr}" |
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47 -ptm_score "${processing_options.ptm_score.ptm_score_selector}" |
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48 #if $processing_options.ptm_score.ptm_score_selector == 1 |
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49 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" |
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50 #if str($processing_options.ptm_score.ptm_threshold) != '' |
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51 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" |
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52 #end if |
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53 #end if |
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54 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" |
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55 -ptm_alignment "${processing_options.ptm_alignment}" |
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56 #end if |
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57 |
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58 ##Optional filtering parameters: |
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59 #if $filtering_options.filtering_options_selector == "yes": |
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60 -import_peptide_length_min "${filtering_options.min_peptide_length}" |
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61 -import_peptide_length_max "${filtering_options.max_peptide_length}" |
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62 -import_precurosor_mz "${filtering_options.max_precursor_error}" |
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63 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}" |
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64 ##-max_xtandem_e "${filtering_options.max_xtandem_e}" |
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65 ##-max_omssa_e "${filtering_options.max_omssa_e}" |
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66 ##-max_mascot_e "${filtering_options.max_mascot_e}" |
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67 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" |
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68 #end if |
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69 |
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70 2>> $temp_stderr) |
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71 |
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72 && |
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73 |
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74 echo "Running Reports"; |
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75 |
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76 ################################## |
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77 ## PeptideShaker Report options ## |
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78 ################################## |
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79 |
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80 #if 'mzidentML' in str($outputs).split(','): |
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81 echo "Generating mzIdentML"; |
18 | 82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI |
83 --exec_dir="\$cwd/${bin_dir}" | |
0
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84 -in \$cwd/peptideshaker_output.zip |
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85 -output_file output.mzid |
18 | 86 #if $contact_options.contact_options_selector == "yes": |
87 -contact_first_name "$contact_options.contact_first_name" | |
88 -contact_last_name "$contact_options.contact_last_name" | |
89 -contact_email "$contact_options.contact_email" | |
90 -contact_address "$contact_options.contact_address" | |
91 #if str($contact_options.contact_url).strip() != '': | |
92 -contact_url = "$contact_options.contact_url" | |
93 #end if | |
94 -organization_name "$contact_options.organization_name" | |
95 -organization_email "$contact_options.organization_email" | |
96 -organization_address "$contact_options.organization_address" | |
97 #if str($contact_options.organization_url).strip() != '': | |
98 -organization_url = "$contact_options.organization_url" | |
99 #end if | |
100 #else: | |
101 -contact_first_name "Proteomics" | |
102 -contact_last_name "Galaxy" | |
103 -contact_email "galaxyp@umn.edu" | |
104 -contact_address "galaxyp@umn.edu" | |
105 -organization_name "University of Minnesota" | |
106 -organization_email "galaxyp@umn.edu" | |
107 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" | |
108 #end if | |
0
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109 2>> $temp_stderr) |
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110 && |
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111 #end if |
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112 |
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113 ## Generate Reports if the user has selected one of the 8 additional reports |
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114 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker |
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115 ## and will not be passed to the command line |
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116 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): |
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117 |
18 | 118 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI |
119 --exec_dir="\$cwd/${bin_dir}" | |
0
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120 -temp_folder \$cwd/ReportCLI |
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121 -in \$cwd/peptideshaker_output.zip |
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122 -out_reports \$cwd/output_reports |
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123 #set $cleaned_list = str($outputs).split(',') |
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124 #if 'cps' in $cleaned_list: |
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125 #silent $cleaned_list.remove('cps') |
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126 #end if |
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127 #if 'mzidentML' in $cleaned_list: |
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128 #silent $cleaned_list.remove('mzidentML') |
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129 #end if |
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130 #if 'zip' in $cleaned_list: |
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131 #silent $cleaned_list.remove('zip') |
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132 #end if |
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133 ## Only numbers are left over. These corresponds to different reports. |
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134 -reports #echo ','.join($cleaned_list)# |
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135 |
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136 2>> $temp_stderr) |
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137 && |
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138 #end if |
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139 |
18 | 140 ## # ls -l \$cwd/output_reports/* ; |
0
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141 |
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142 #if '0' in str($outputs).split(','): |
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143 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; |
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144 ; |
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145 #end if |
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146 #if '1' in str($outputs).split(','): |
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147 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; |
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148 ; |
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149 #end if |
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150 #if '2' in str($outputs).split(','): |
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151 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; |
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152 ; |
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153 #end if |
18 | 154 #if '8' in str($outputs).split(','): |
155 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \; | |
156 ; | |
157 #end if | |
0
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158 #if '3' in str($outputs).split(','): |
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159 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; |
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160 ; |
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161 #end if |
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162 #if '4' in str($outputs).split(','): |
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163 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \; |
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164 ; |
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165 #end if |
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166 #if '5' in str($outputs).split(','): |
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167 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; |
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168 ; |
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169 #end if |
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170 #if '6' in str($outputs).split(','): |
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171 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \; |
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172 ; |
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173 #end if |
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174 #if '7' in str($outputs).split(','): |
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175 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; |
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176 ; |
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177 #end if |
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178 |
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179 exit_code_for_galaxy=\$?; |
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180 cat $temp_stderr 2>&1; |
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181 (exit \$exit_code_for_galaxy) |
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182 |
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183 ]]> |
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184 </command> |
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185 <inputs> |
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186 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" |
13 | 187 help="SearchGUI Results from History"> |
188 <options options_filter_attribute="metadata.searchgui_major_version" > | |
189 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> | |
190 </options> | |
191 </param> | |
0
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192 <conditional name="processing_options"> |
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193 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> |
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194 <option value="no" selected="True">Default Processing Options</option> |
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195 <option value="yes">Advanced Processing Options</option> |
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196 </param> |
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197 <when value="no" /> |
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198 <when value="yes"> |
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199 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
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200 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
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201 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
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202 <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" |
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203 help="default 95%: '95.0'" /> |
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204 <conditional name="ptm_score"> |
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205 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> |
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206 <option value="0" selected="True">A-score</option> |
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207 <option value="1">PhosphoRS</option> |
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208 </param> |
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209 <when value="0" /> |
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210 <when value="1"> |
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211 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> |
16
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212 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" |
0
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213 help="Automatic mode will be used if not set" /> |
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214 </when> |
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215 </conditional> |
17
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216 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> |
0
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217 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> |
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218 </when> |
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219 </conditional> |
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220 <conditional name="filtering_options"> |
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221 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" |
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222 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"> |
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223 <option value="no" selected="True">Default Filtering Options</option> |
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224 <option value="yes">Advanced Filtering Options</option> |
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225 </param> |
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226 <when value="no" /> |
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227 <when value="yes"> |
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228 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> |
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229 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> |
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230 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" |
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231 help="Next option specifies units (Da or ppm)" /> |
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232 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> |
17
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233 <option value="1">ppm</option> |
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234 <option value="0">Daltons</option> |
0
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235 </param> |
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236 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> |
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237 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> |
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238 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> |
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239 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
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240 </when> |
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241 </conditional> |
18 | 242 <conditional name="contact_options"> |
243 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML" | |
244 help="Create a Galaxy workflow to save these values"> | |
245 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option> | |
246 <option value="yes">Specify Contact Information</option> | |
247 </param> | |
248 <when value="no" /> | |
249 <when value="yes"> | |
250 <param name="contact_first_name" type="text" value="" label="Contact first name."> | |
251 <validator type="regex" message="">\S+.*</validator> | |
252 </param> | |
253 <param name="contact_last_name" type="text" value="" label="Contact last name."> | |
254 <validator type="regex" message="">\S+.*</validator> | |
255 </param> | |
256 <param name="contact_email" type="text" value="" label="Contact e-mail."> | |
257 <validator type="regex" message="">\S+@\S+</validator> | |
258 </param> | |
259 <param name="contact_address" type="text" value="" label="Contact address."> | |
260 <validator type="regex" message="">\S+.*</validator> | |
261 </param> | |
262 <param name="contact_url" type="text" value="" optional="true" label="Contact URL."> | |
263 </param> | |
264 <param name="organization_name" type="text" value="" label="Organization name."> | |
265 <validator type="regex" message="">\S+.*</validator> | |
266 </param> | |
267 <param name="organization_email" type="text" value="" label="Organization e-mail."> | |
268 <validator type="regex" message="">\S+@\S+</validator> | |
269 </param> | |
270 <param name="organization_address" type="text" value="" label="Organization address."> | |
271 <validator type="regex" message="">\S+.*</validator> | |
272 </param> | |
273 <param name="organization_url" type="text" value="" optional="true" label="Organization URL."> | |
274 </param> | |
275 </when> | |
276 </conditional> | |
277 | |
278 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" /> | |
0
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279 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> |
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280 <option value="zip">Zip File for import to Desktop App</option> |
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281 <option value="mzidentML" selected="True">mzidentML File</option> |
18 | 282 <option value="3">PSM Report</option> |
283 <option value="8">Extended PSM Report</option> | |
0
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284 <option value="2">PSM Phosphorylation Report</option> |
18 | 285 <option value="5">Peptide Report</option> |
286 <option value="4">Peptide Phosphorylation Report</option> | |
287 <option value="7">Protein Report</option> | |
288 <option value="6">Protein Phosphorylation Report</option> | |
0
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289 <option value="0">Certificate of Analysis</option> |
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290 <option value="1">Hierarchical Report</option> |
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291 <option value="cps">CPS file</option> |
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292 <validator type="no_options" message="Please select at least one output file" /> |
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293 </param> |
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294 |
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295 </inputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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296 <outputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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297 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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298 <filter>'mzidentML' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
299 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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300 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
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301 <filter>'cps' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
302 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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303 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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304 <filter>'zip' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
305 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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306 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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307 <filter>'0' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
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308 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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309 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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310 <filter>'1' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
311 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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312 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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313 <filter>'2' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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314 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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315 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
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316 <filter>'3' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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317 </data> |
18 | 318 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> |
319 <filter>'8' in outputs</filter> | |
320 </data> | |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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321 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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322 <filter>'4' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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323 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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324 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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325 <filter>'5' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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326 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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327 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
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328 <filter>'6' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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329 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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330 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
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331 <filter>'7' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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332 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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333 </outputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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334 <tests> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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335 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
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|
336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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337 <param name="species_type_selector" value="no_species_type"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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338 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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339 <param name="filtering_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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340 <param name="outputs" value="zip,cps,3"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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341 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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342 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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343 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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344 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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345 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
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346 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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347 <param name="species_type_selector" value="no_species_type"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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348 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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349 <param name="filtering_options_selector" value="yes"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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350 <param name="min_peptide_length" value="1"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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351 <param name="outputs" value="0,1,2,3,4,5,6,7"/> |
10
9d12b1d3c4ef
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9
iracooke
parents:
6
diff
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352 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
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353 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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354 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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changeset
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355 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
356 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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changeset
|
357 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
358 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
359 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
360 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
361 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
changeset
|
362 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
363 <param name="species_type_selector" value="Vertebrates"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
364 <param name="species" value="Human (Homo sapiens)"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
365 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
366 <param name="filtering_options_selector" value="yes"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
367 <param name="min_peptide_length" value="1"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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368 <param name="outputs" value="5"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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369 <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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370 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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371 </tests> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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372 <help> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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373 **What it does** |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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374 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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375 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. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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376 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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377 https://code.google.com/p/peptide-shaker/ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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378 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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379 https://code.google.com/p/searchgui/ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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380 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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381 ---- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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382 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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383 Reports |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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384 ======= |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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385 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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386 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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387 PSM Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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388 ---------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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389 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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390 * Protein(s): Protein(s) to which the peptide can be attached |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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391 * Sequence: Sequence of the peptide |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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392 * Variable Modifications: The variable modifications |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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393 * D-score: D-score for variable PTM localization |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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394 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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395 * Localization Confidence: The confidence in variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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396 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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397 * Spectrum File: The spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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398 * Spectrum Title: The title of the spectrum. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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399 * Spectrum Scan Number: The spectrum scan number. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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400 * RT: Retention time |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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401 * m/z: Measured m/z |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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402 * Measured Charge: The charge as given in the spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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403 * Identification Charge: The charge as inferred by the search engine. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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404 * Theoretical Mass: The theoretical mass of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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405 * Isotope Number: The isotope number targetted by the instrument. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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406 * Precursor m/z Error: The precursor m/z matching error. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
407 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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408 * Confidence: Confidence in percent associated to the retained PSM. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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409 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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410 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
411 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
412 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
413 Protein Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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|
414 -------------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
415 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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416 * Main Accession: Main accession of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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417 * Description: Description of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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418 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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419 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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420 * PI: Protein Inference status of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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421 * Secondary Accessions: Other accessions in the protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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422 * Protein Group: The complete protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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423 * #Peptides: Total number of peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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424 * #Validated Peptides: Number of validated peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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425 * #Unique: Total number of peptides unique to this protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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426 * #PSMs: Number of PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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427 * #Validated PSMs: Number of validated PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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428 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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429 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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430 * MW (kDa): Molecular Weight. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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431 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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432 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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433 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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434 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
435 * Score: Score of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
436 * Confidence: Confidence in percent associated to the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
437 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
438 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
439 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
440 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
441 Peptide Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
442 -------------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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443 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
444 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
445 * Protein(s): Protein(s) to which this peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
446 * AAs Before: The amino-acids before the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
447 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
448 * AAs After: The amino-acids after the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
449 * Modified Sequence: The peptide sequence annotated with variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
450 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
451 * Localization Confidence: The confidence in PTMs localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
452 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
453 * #Validated PSMs: Number of validated PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
454 * #PSMs: Number of PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
455 * Score: Score of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
456 * Confidence: Confidence in percent associated to the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
457 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
458 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
459 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
460 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
461 Hierachical Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
462 ------------------ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
463 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
464 * Main Accession: Main accession of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
465 * Description: Description of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
466 * PI: Protein Inference status of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
467 * Secondary Accessions: Other accessions in the protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
468 * Protein Group: The complete protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
469 * #Peptides: Total number of peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
470 * #Validated Peptides: Number of validated peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
471 * #Unique: Total number of peptides unique to this protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
472 * #PSMs: Number of PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
473 * #Validated PSMs: Number of validated PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
474 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
475 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
476 * MW (kDa): Molecular Weight. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
477 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
478 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
479 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
480 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
481 * Score: Score of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
482 * Confidence: Confidence in percent associated to the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
483 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
484 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
485 * Protein(s): Protein(s) to which this peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
486 * AAs Before: The amino-acids before the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
487 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
488 * AAs After: The amino-acids after the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
489 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
490 * Localization Confidence: The confidence in PTMs localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
491 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
492 * #Validated PSMs: Number of validated PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
493 * #PSMs: Number of PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
494 * Score: Score of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
495 * Confidence: Confidence in percent associated to the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
496 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
497 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
498 * Protein(s): Protein(s) to which the peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
499 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
500 * Modified Sequence: The peptide sequence annotated with variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
501 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
502 * D-score: D-score for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
503 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
504 * Localization Confidence: The confidence in variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
505 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
506 * Spectrum File: The spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
507 * Spectrum Title: The title of the spectrum. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
508 * Spectrum Scan Number: The spectrum scan number. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
509 * RT: Retention time |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
510 * m/z: Measured m/z |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
511 * Measured Charge: The charge as given in the spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
512 * Identification Charge: The charge as inferred by the search engine. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
513 * Theoretical Mass: The theoretical mass of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
514 * Isotope Number: The isotope number targetted by the instrument. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
515 * Precursor m/z Error: The precursor m/z matching error. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
516 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
517 * Confidence: Confidence in percent associated to the retained PSM. |
a9e90cdcb97a
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518 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
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519 * Validation: Indicates the validation level of the protein group. |
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520 |
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521 |
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522 ------ |
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523 |
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524 **Citation** |
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525 |
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526 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com |
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527 |
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528 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker |
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529 </help> |
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530 <expand macro="citations" /> |
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531 </tool> |