Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 54:7fdd9119cc4f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6"
author galaxyp
date Thu, 20 Feb 2020 05:51:38 -0500
parents d67a3c1bfd09
children bb0130ff73ce
comparison
equal deleted inserted replaced
53:d67a3c1bfd09 54:7fdd9119cc4f
28 ln -s '$searchgui_input' searchgui_input.zip && 28 ln -s '$searchgui_input' searchgui_input.zip &&
29 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && 29 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
30 30
31 31
32 peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI 32 peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI
33 --exec_dir="\$cwd/${bin_dir}" 33 --exec_dir="\$cwd/${bin_dir}"
34 -temp_folder \$cwd/PathSettingsCLI 34 -temp_folder \$cwd/PathSettingsCLI
35 -log \$cwd/peptideshaker.log && 35 -log \$cwd/peptideshaker.log &&
36 36
37 #if str($exporting_options.output_reports) != "None" 37 #if str($exporting_options.output_reports) != "None"
38 #set $output_reports_list = set(str($exporting_options.output_reports).split(',')) 38 #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
39 #else 39 #else
40 #set $output_reports_list = set() 40 #set $output_reports_list = set()
41 #end if 41 #end if
42 42
43 ###################### 43 ######################
44 ## PeptideShakerCLI ## 44 ## PeptideShakerCLI ##
45 ###################### 45 ######################
46 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI 46 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
51 -sample '$samp_str' 51 -sample '$samp_str'
52 -replicate 1 52 -replicate 1
53 -identification_files \$cwd/searchgui_input.zip 53 -identification_files \$cwd/searchgui_input.zip
54 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par 54 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
55 -out \$cwd/peptideshaker_output.cpsx 55 -out \$cwd/peptideshaker_output.cpsx
56 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip': 56 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
57 -zip \$cwd/peptideshaker_output.zip 57 -zip \$cwd/peptideshaker_output.zip
58 #end if 58 #end if
59 -threads "\${GALAXY_SLOTS:-12}" 59 -threads "\${GALAXY_SLOTS:-12}"
60 60
61 ##Optional processing parameters: 61 ##Optional processing parameters:
62 #if $processing_options.processing_options_selector == "yes" 62 #if $processing_options.processing_options_selector == "yes"
63 -protein_fdr "${processing_options.protein_fdr}" 63 -protein_fdr "${processing_options.protein_fdr}"
133 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them 133 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
134 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip: 134 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip:
135 && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports 135 && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports
136 #end if 136 #end if
137 137
138 #if len(output_reports_list)>0: 138 #if len($output_reports_list)>0:
139 #if '0' in $output_reports_list: 139 #if '0' in $output_reports_list:
140 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; 140 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
141 #end if 141 #end if
142 #if '1' in $output_reports_list: 142 #if '1' in $output_reports_list:
143 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; 143 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
144 #end if 144 #end if
145 #if '2' in $output_reports_list: 145 #if '2' in $output_reports_list:
146 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; 146 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
147 #end if` 147 #end if
148 #if '3' in $output_reports_list: 148 #if '3' in $output_reports_list:
149 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; 149 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
150 #end if 150 #end if
151 #if '4' in $output_reports_list: 151 #if '4' in $output_reports_list:
152 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \; 152 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;