Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 56:1beff3ddce58 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"
author galaxyp
date Wed, 20 Jan 2021 13:29:07 +0000
parents bb0130ff73ce
children da885ca16cb2
comparison
equal deleted inserted replaced
55:bb0130ff73ce 56:1beff3ddce58
20 #set $temp_stderr = "searchgui_stderr" 20 #set $temp_stderr = "searchgui_stderr"
21 #set $bin_dir = "bin" 21 #set $bin_dir = "bin"
22 22
23 mkdir output; 23 mkdir output;
24 mkdir output_reports; 24 mkdir output_reports;
25 mkdir temp_folder;
26 mkdir log_folder;
25 cwd=`pwd`; 27 cwd=`pwd`;
26 export HOME=\$cwd; 28 export HOME=\$cwd;
27 29
28 echo "" > $temp_stderr && 30 echo "" > $temp_stderr &&
29 31
61 --exec_dir="\$cwd/${bin_dir}" 63 --exec_dir="\$cwd/${bin_dir}"
62 -spectrum_files \$cwd 64 -spectrum_files \$cwd
63 -fasta_file "\$cwd/input_fasta_file.fasta" 65 -fasta_file "\$cwd/input_fasta_file.fasta"
64 -output_folder \$cwd/output 66 -output_folder \$cwd/output
65 -id_params ./SEARCHGUI_IdentificationParameters.par 67 -id_params ./SEARCHGUI_IdentificationParameters.par
66 68 -temp_folder \$cwd/temp_folder
69 -log \$cwd/log_folder
67 -threads "\${GALAXY_SLOTS:-12}" 70 -threads "\${GALAXY_SLOTS:-12}"
68 71
69 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' 72 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
70 -correct_titles "${searchgui_advanced.correct_titles}" 73 -correct_titles "${searchgui_advanced.correct_titles}"
71 $searchgui_advanced.missing_titles 74 $searchgui_advanced.missing_titles