Mercurial > repos > galaxyp > peptideshaker
changeset 47:44ca2967218c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
| author | galaxyp |
|---|---|
| date | Sat, 15 Sep 2018 08:51:12 -0400 |
| parents | baeced706dbc |
| children | 64e3a8cc8ffb |
| files | macros.xml searchgui.xml |
| diffstat | 2 files changed, 43 insertions(+), 47 deletions(-) [+] |
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--- a/macros.xml Wed Jul 11 08:14:23 2018 -0400 +++ b/macros.xml Sat Sep 15 08:51:12 2018 -0400 @@ -2,7 +2,10 @@ <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="java.*Exception" level="fatal" description="Java Exception"/> + <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/> + <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> + <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> + <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> @@ -55,51 +58,31 @@ <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> <conditional name="digestion"> <param name="cleavage" type="select" label="Digestion"> - <option value="default" selected="true">Trypsin</option> <option value="0">Select Enzymes</option> <option value="1">Unspecific Cleavage</option> <option value="2">Whole Protein</option> </param> - <when value="default"> - <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" - help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> - </when> <when value="0"> <repeat name="digests" min="1" title="Enzymes"> <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> <option value="Trypsin">Trypsin</option> + <option value="Trypsin (no P rule)">Trypsin (no P rule)</option> <option value="Arg-C">Arg-C</option> - <option value="CNBr">CNBr</option> - <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> - <option value="Formic Acid">Formic Acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-C, no P rule">Lys-C, no P rule</option> - <option value="Pepsin A">Pepsin A</option> - <option value="Trypsin + CNBr">Trypsin + CNBr</option> - <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> - <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="Whole Protein">Whole Protein</option> - <option value="Asp-N">Asp-N</option> + <option value="Arg-C (no P rule)">Arg-C</option> + <option value="Arg-N">Arg-N</option> <option value="Glu-C">Glu-C</option> - <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> - <option value="Top-Down">Top-Down</option> - <option value="Semi-Tryptic">Semi-Tryptic</option> - <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> - <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> - <option value="Asp-N (DE)">Asp-N (DE)</option> - <option value="Glu-C (DE)">Glu-C (DE)</option> - <option value="Lys-N (K)">Lys-N (K)</option> - <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> - <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> - <option value="Semi-Glu-C">Semi-Glu-C</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C (no P rule)">Lys-C (no P rule)</option> + <option value="Lys-N">Lys-N</option> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N (ambic)">Asp-N (ambic)</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option> + <option value="Pepsin A">Pepsin A</option> + <option value="CNBr">CNBr</option> + <option value="Thermolysin">Thermolysin</option> <option value="LysargiNase">LysargiNase</option> - <option value="Semi-LysargiNase">Semi-LysargiNase</option> - <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> - <option value="Semi-Arg-C">Semi-Arg-C</option> - <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> - <option value="Arg-N">Arg-N</option> - <option value="Semi-Arg-N">Semi-Arg-N</option> </param> <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
--- a/searchgui.xml Wed Jul 11 08:14:23 2018 -0400 +++ b/searchgui.xml Sat Sep 15 08:51:12 2018 -0400 @@ -6,11 +6,11 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> - <requirement type="package" version="3.0">zip</requirement> + <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <requirement type="package" version="3.0">zip</requirement> </requirements> <expand macro="stdio" /> - <command> + <command use_shared_home="false"> <![CDATA[ #from datetime import datetime #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") @@ -23,28 +23,40 @@ cwd=`pwd`; export HOME=\$cwd; - ## echo the search engines to run - echo "$search_engines_options.engines"; - echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; + ## echo the search engines to run (single quotes important because X!Tandem) + echo '$search_engines_options.engines'; + echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}'; ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present - echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; + echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties; #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; #set $encoded_id = $__app__.security.encode_id($mgf.id) - echo "Spectrums:${mgf.display_name}(API:${encoded_id}) "; + echo 'Spectrums:${mgf.display_name}(API:${encoded_id})'; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta; ########################################### + #### Set paths #### + ########################################### + echo 'Setting paths' && + searchgui eu.isas.searchgui.cmd.PathSettingsCLI + --exec_dir="\$cwd/${bin_dir}" + -temp_folder \$cwd + -log \$cwd/searchgui.log 2>> $temp_stderr && + + ########################################### #### Creating decoy database #### ########################################### #if $protein_database_options.create_decoy: - echo "Creating decoy database."; - searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy && + echo 'Creating decoy database.' && + searchgui eu.isas.searchgui.cmd.FastaCLI + --exec_dir="\$cwd/${bin_dir}" + -in input_database.fasta + -decoy 2>> $temp_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta && ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; @@ -53,6 +65,7 @@ ##################################################### ## generate IdentificationParameters for SearchGUI ## ##################################################### + echo 'setting identification parameters' && (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="\$cwd/${bin_dir}" -out SEARCHGUI_IdentificationParameters.par @@ -323,9 +336,9 @@ ################ ## Search CLI ## ################ + echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="\$cwd/${bin_dir}" - -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output -id_params SEARCHGUI_IdentificationParameters.par @@ -1097,7 +1110,7 @@ <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> <param name="xtandem.xtandem_advanced" value="yes"/> <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> - <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> + <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> <!-- Test that search works with MSAmanda --> <test> @@ -1107,7 +1120,7 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> - <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> <!-- Test that specifying non-default search engines works using modifications -->