Mercurial > repos > galaxyp > peptideshaker
diff searchgui.xml @ 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 |
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--- 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>