Mercurial > repos > galaxyp > peptideshaker
comparison peptide_shaker.xml @ 53:166173739c8d draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003"
| author | galaxyp |
|---|---|
| date | Tue, 20 Jul 2021 08:54:32 +0000 |
| parents | c506a7ccb856 |
| children |
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| 52:c506a7ccb856 | 53:166173739c8d |
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| 36 ## OPTIONAL MAIN PARAMETERS | 36 ## OPTIONAL MAIN PARAMETERS |
| 37 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file | 37 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file |
| 38 #if $optional_main_parameters.input_optional_identification_parameters: | 38 #if $optional_main_parameters.input_optional_identification_parameters: |
| 39 cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par && | 39 cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par && |
| 40 #else: | 40 #else: |
| 41 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && | 41 ## Note that there will be just one .par file, the one (with unkown name) used thorought SG execution. We will rename it to a "standard" name |
| 42 unzip -o searchgui_input.zip *.par && | |
| 43 mv *.par SEARCHGUI_IdentificationParameters.par && | |
| 42 #end if | 44 #end if |
| 43 ## Optional Fasta file | 45 ## Optional Fasta file |
| 44 #if $optional_main_parameters.input_fasta_file: | 46 #if $optional_main_parameters.input_fasta_file: |
| 45 ## copy the input .fasta file to the working folder | 47 ## copy the input .fasta file to the working folder |
| 46 cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' && | 48 cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' && |
| 66 #end if | 68 #end if |
| 67 | 69 |
| 68 ###################### | 70 ###################### |
| 69 ## PeptideShakerCLI ## | 71 ## PeptideShakerCLI ## |
| 70 ###################### | 72 ###################### |
| 71 | 73 |
| 72 ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package). | 74 ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package). |
| 73 | 75 |
| 74 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI | 76 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI |
| 75 -gui 0 | 77 -gui 0 |
| 76 -temp_folder \$cwd/PeptideShakerCLI | 78 -temp_folder \$cwd/PeptideShakerCLI |
| 186 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window | 188 #if $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 | 189 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window |
| 188 #end if | 190 #end if |
| 189 #end if | 191 #end if |
| 190 #end if | 192 #end if |
| 191 | 193 |
| 192 ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)" | 194 ## 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 | 195 ## is fixed , we can avoid the process to be stopped by removing that message from the output |
| 194 | 196 |
| 195 | grep -v "resources/conf/paths.txt (Permission denied)" | 197 | grep -v "resources/conf/paths.txt (Permission denied)" |
| 196 | 198 |
| 197 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them | 199 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them |
| 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): | 200 #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): |
| 199 ## This unzipping command creates a reports folder into the current folder! | 201 ## This unzipping command creates a reports folder into the current folder! |
| 200 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd | 202 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd |
| 201 && mv reports/* output_reports | 203 && mv reports/* output_reports |