Mercurial > repos > galaxyp > peptideshaker
changeset 57:da885ca16cb2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
| author | galaxyp |
|---|---|
| date | Tue, 16 Mar 2021 15:12:03 +0000 |
| parents | 1beff3ddce58 |
| children | 07ff622ec007 |
| files | fasta_cli.xml ident_params.xml macros_basic.xml peptide_shaker.xml searchgui.xml |
| diffstat | 5 files changed, 53 insertions(+), 42 deletions(-) [+] |
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--- a/fasta_cli.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/fasta_cli.xml Tue Mar 16 15:12:03 2021 +0000 @@ -1,4 +1,8 @@ -<tool id="fasta_cli" name="FastaCLI" version="1.0.1"> +<tool id="fasta_cli" + name="FastaCLI" + version="1.0.1" + profile="20.01" +> <description> Appends decoy sequences to FASTA files </description> @@ -11,7 +15,6 @@ <expand macro="stdio" /> <command> <![CDATA[ - #set $temp_stderr = "fasta_cli_stderr" #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta" mkdir output && @@ -25,9 +28,8 @@ ########################################### echo 'Creating decoy database.' && - searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag 2>> $temp_stderr && - mv '${output_db_name}' output && - cat $temp_stderr 2>&1; + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag && + mv '${output_db_name}' output ]]> </command> <inputs>
--- a/ident_params.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/ident_params.xml Tue Mar 16 15:12:03 2021 +0000 @@ -1,4 +1,8 @@ -<tool id="ident_params" name="Identification Parameters" version="1.5.1"> +<tool id="ident_params" + name="Identification Parameters" + version="1.5.1" + profile="20.01" +> <description> Sets the identification parameters to be used in SearchGUI and PeptideShaker apps </description> @@ -12,7 +16,6 @@ <expand macro="stdio" /> <command> <![CDATA[ - #set $temp_stderr = "searchgui_stderr" #set $bin_dir = "bin" mkdir output; @@ -20,13 +23,12 @@ export HOME=\$cwd; - echo "" > $temp_stderr && echo 'running Identification Parameters CLI' && ##################################################### ## generate IdentificationParameters for SearchGUI ## ##################################################### - (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="./bin/" -out './IdentificationParametersOutput.par' @@ -614,10 +616,6 @@ #end if -fasta_target_decoy 0 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag - - 2> $temp_stderr) && - - cat $temp_stderr 2>&1; ]]> </command> <inputs>
--- a/macros_basic.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/macros_basic.xml Tue Mar 16 15:12:03 2021 +0000 @@ -2,17 +2,18 @@ <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> + <regex match="OutOfMemoryError" level="fatal_oom" description="Out of memory"/> <regex match="java.*Exception" level="fatal" description="Java Exception"/> - <regex match="Could not reserve enough space for * object heap" level="fatal" description="Out of memory"/> + <regex match="Could not reserve enough space for * object heap" level="fatal_oom" description="Out of memory"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> - <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/> + <regex match="PeptideShaker ran out of memory" level="fatal_oom" description="JVM Error"/> <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> </xml> <token name="@SEARCHGUI_MAJOR_VERSION@">4</token> - <token name="@SEARCHGUI_VERSION@">4.0.12</token> + <token name="@SEARCHGUI_VERSION@">4.0.22</token> <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token> - <token name="@PEPTIDESHAKER_VERSION@">2.0.9</token> + <token name="@PEPTIDESHAKER_VERSION@">2.0.15</token> <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token> <xml name="citations"> <citations>
--- a/peptide_shaker.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/peptide_shaker.xml Tue Mar 16 15:12:03 2021 +0000 @@ -1,4 +1,9 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"> +<tool id="peptide_shaker" + name="Peptide Shaker" + version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@" + profile="20.01" +> + <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -11,22 +16,23 @@ <requirement type="package">unzip</requirement> </requirements> <expand macro="stdio" /> - - <command><![CDATA[ - ## When supporting more advanced Galaxy versions: command use_shared_home="false" + <!-- TODO: check trap comment. + <command use_shared_home="false"> +--> + <command> +<![CDATA[ #from datetime import datetime #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") - #set $temp_stderr = "peptideshaker_stderr" #set $bin_dir = "bin" #set $exporting_followup_boolean = False + ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file. + ## trap ">&2 cat resources/*.log" EXIT; mkdir output_reports && cwd=`pwd` && export HOME=\$cwd && - echo "" > $temp_stderr && - ln -s '$searchgui_input' searchgui_input.zip && ## OPTIONAL MAIN PARAMETERS @@ -64,7 +70,7 @@ ###################### ## PeptideShakerCLI ## ###################### - (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI + peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI -gui 0 -temp_folder \$cwd/PeptideShakerCLI -log \$cwd/resources @@ -182,8 +188,6 @@ #end if #end if - 2>> $temp_stderr) - ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them #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): ## This unzipping command creates a reports folder into the current folder! @@ -238,6 +242,10 @@ #if '11' in $output_reports_list: && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \; #end if + ## the last ; is removed from the generated command line + ## thus we need to make sure that the above `find ... -exec ... \;` + ## is not the last command + && true #end if ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip) @@ -259,7 +267,6 @@ && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt #end if #end if - && cat $temp_stderr 2>&1; ]]> </command> <inputs> @@ -626,7 +633,6 @@ <has_line_matching expression="520.9862671 4666.4399414063"/> <has_line_matching expression="267.4349976 50.7710571289"/> <has_line_matching expression="665.7418213 3.8165459633"/> - <has_line_matching expression="672.2329102 146.2656707764"/> <has_line_matching expression="634.7792969 2367.6374511719"/> </assert_contents> </element>
--- a/searchgui.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/searchgui.xml Tue Mar 16 15:12:03 2021 +0000 @@ -1,4 +1,8 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"> +<tool id="search_gui" + name="Search GUI" + version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@" + profile="20.01" +> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -11,24 +15,24 @@ </requirements> <expand macro="stdio" /> <command use_shared_home="false"> + <![CDATA[ #from datetime import datetime #import json #import os #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") - #set $temp_stderr = "searchgui_stderr" #set $bin_dir = "bin" mkdir output; mkdir output_reports; mkdir temp_folder; mkdir log_folder; + trap ">&2 cat log_folder/*.log" EXIT; + cwd=`pwd`; export HOME=\$cwd; - echo "" > $temp_stderr && - ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}'; @@ -59,7 +63,7 @@ ## Search CLI ## ################ echo 'running search gui' && - (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="\$cwd/${bin_dir}" -spectrum_files \$cwd -fasta_file "\$cwd/input_fasta_file.fasta" @@ -150,17 +154,17 @@ ## mgf and database in output -output_data 1 - 2>> $temp_stderr) + && + + echo '>log_folder:' && + + ls -l \$cwd/log_folder && + + mv output/searchgui_out.zip searchgui_out.zip && - (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) - - && - - (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); - - cat $temp_stderr 2>&1; + zip -u searchgui_out.zip searchgui.properties ]]> </command> <inputs>