Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 59:943a34df6047 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
author galaxyp
date Fri, 21 May 2021 19:13:14 +0000
parents 07ff622ec007
children a6ff76e057fd
comparison
equal deleted inserted replaced
58:07ff622ec007 59:943a34df6047
24 #from datetime import datetime 24 #from datetime import datetime
25 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 25 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
26 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 26 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
27 #set $bin_dir = "bin" 27 #set $bin_dir = "bin"
28 #set $exporting_followup_boolean = False 28 #set $exporting_followup_boolean = False
29 ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
30 ## trap ">&2 cat resources/*.log" EXIT;
31 29
32 mkdir output_reports && 30 mkdir output_reports &&
33 cwd=`pwd` && 31 cwd=`pwd` &&
34 export HOME=\$cwd && 32 export HOME=\$cwd &&
35 33
68 #end if 66 #end if
69 67
70 ###################### 68 ######################
71 ## PeptideShakerCLI ## 69 ## PeptideShakerCLI ##
72 ###################### 70 ######################
71
72 ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package).
73
73 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI 74 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
74 -gui 0 75 -gui 0
75 -temp_folder \$cwd/PeptideShakerCLI 76 -temp_folder \$cwd/PeptideShakerCLI
76 -log \$cwd/resources 77 -use_log_folder 0
77 -reference '$exp_str' 78 -reference '$exp_str'
78 -identification_files \$cwd/searchgui_input.zip 79 -identification_files \$cwd/searchgui_input.zip
79 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par 80 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
80 #if $optional_main_parameters.input_fasta_file: 81 #if $optional_main_parameters.input_fasta_file:
81 -fasta_file './input_fasta_file.fasta' 82 -fasta_file './input_fasta_file.fasta'
185 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window 186 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
186 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window 187 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
187 #end if 188 #end if
188 #end if 189 #end if
189 #end if 190 #end if
190 191
192 ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)"
193 ## is fixed , we can avoid the process to be stopped by removing that message from the output
194
195 | grep -v "resources/conf/paths.txt (Permission denied)"
196
191 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them 197 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
192 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean): 198 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
193 ## This unzipping command creates a reports folder into the current folder! 199 ## This unzipping command creates a reports folder into the current folder!
194 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd 200 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
195 && mv reports/* output_reports 201 && mv reports/* output_reports