Mercurial > repos > jjohnson > peptideshaker
diff searchgui.xml @ 0:8b99cb00e1c4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
| author | jjohnson |
|---|---|
| date | Tue, 15 May 2018 14:50:35 -0400 |
| parents | |
| children | fa76abf69433 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui.xml Tue May 15 14:50:35 2018 -0400 @@ -0,0 +1,285 @@ +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> + <description> + Perform protein identification using various search engines and prepare results for input to Peptide Shaker + </description> + <macros> + <import>macros_basic.xml</import> + </macros> + <requirements> + <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <requirement type="package" version="3.0">zip</requirement> + <requirement type="package">JQ</requirement> + </requirements> + <expand macro="stdio" /> + <command> +<![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 $bin_dir = "bin" + + mkdir output; + mkdir output_reports; + cwd=`pwd`; + export HOME=\$cwd; + + ## echo the search engines to run + echo "$search_engines_options.engines"; + + ##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; + + #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}) "; + #end for + + + + ## Necessary for executing tests. The FASTA file has to be manually copied from the test-data folder to the working directory in order it can be found when using the PAR file. + cp '$__tool_directory__/test-data/searchgui_tinydb1_concatenated_target_decoy.fasta' "\$cwd/searchgui_tinydb1_concatenated_target_decoy.fasta"; + + + + ## copy the input .par file to the working folder + cp "${input_par}" "\$cwd/SEARCHGUI_IdentificationParameters.par"; + echo "-.par source file:"; + echo "${input_par}"; + + ## (local) PAR file points to a FASTA file with .dat extension, which gives problems with many search engines. We should rename it to a .fasta file before passing it to SearchGUI + #set $par_target_path = "$cwd/SEARCHGUI_IdentificationParameters.par"; + echo "-.par target file:"; + echo $par_target_path; + + ## reading from the original .par file the path of the source .dat (fasta) file to be used + content_par_target_path=`cat $par_target_path`; + dat_path=`jq -r '.searchParameters.fastaFile.path' <<< "\$content_par_target_path"`; + echo "-.dat file path from target .par: "; + echo "\$dat_path"; + + ## copy original .data fasta file to a local .fasta file + new_fasta_file_path="\$cwd/input_database.fasta"; + cp "\$dat_path" "\$new_fasta_file_path"; + echo "-new .fasta file path copied from source .dat file: "; + echo "\$new_fasta_file_path"; + + ## modifying the .par file!! + ## First we establish the new content for the path: .searchParameters.fastaFile.path + new_content_par_target_path=`jq '.searchParameters.fastaFile.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$content_par_target_path"`; + ## Secondly, for .proteinInferencePreferences.proteinSequenceDatabase.path + new_content_par_target_path=`jq '.proteinInferencePreferences.proteinSequenceDatabase.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$new_content_par_target_path"`; + + ## we generate a new .par file filled with the new fasta path. + #set $new_par_target_path = "$cwd/SEARCHGUI_IdentificationParameters_new.par"; + echo "\$new_content_par_target_path" >> $new_par_target_path; + echo "-new par target path: "; + echo $new_par_target_path; + + ## As PeptideShaker waits for "SEARCHGUI_IdentificationParameters.par" name, we overwrite the original file with the "_new" file + ##mv "\$cwd/SEARCHGUI_IdentificationParameters_new.par" "\$cwd/SEARCHGUI_IdentificationParameters.par" + rm $par_target_path; + mv $new_par_target_path $par_target_path; + + + ################ + ## Search CLI ## + ################ + (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI + --exec_dir="\$cwd/${bin_dir}" + -temp_folder `pwd` + -spectrum_files \$cwd + -output_folder \$cwd/output + -id_params $par_target_path + + -threads "\${GALAXY_SLOTS:-12}" + + #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' + -correct_titles "${searchgui_advanced.correct_titles}" + $searchgui_advanced.missing_titles + -mgf_splitting "${searchgui_advanced.mgf_splitting}" + -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" + #end if + + ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created + ## the tree is generated afterwards in PeptideShaker + ## -protein_index 0 + + ##-makeblastdb_folder \$BLAST_ROOT_DIR + + #set $engines_list = str($search_engines_options.engines).split(',') + #if 'X!Tandem' in $engines_list: + -xtandem 1 + #else + -xtandem 0 + #end if + + #if 'MyriMatch' in $engines_list: + -myrimatch 1 + #else + -myrimatch 0 + #end if + + #if 'MSGF' in $engines_list: + -msgf 1 + #else + -msgf 0 + #end if + + #if 'OMSSA' in $engines_list: + -omssa 1 + #else + -omssa 0 + #end if + + #if 'Comet' in $engines_list: + -comet 1 + #else + -comet 0 + #end if + + #if 'Tide' in $engines_list: + -tide 1 + #else + -tide 0 + #end if + + #if 'MS_Amanda' in $engines_list: + -ms_amanda 1 + #else + -ms_amanda 0 + #end if + + #if 'Andromeda' in $engines_list: + -andromeda 1 + #else + -andromeda 0 + #end if + + #if 'Novor' in $engines_list: + -novor 1 + #else + -novor 0 + #end if + + #if 'DirecTag' in $engines_list: + -directag 1 + #else + -directag 0 + #end if + + ## single zip file + -output_option 0 + + ## mgf and database in output + -output_data 1 + + 2>> $temp_stderr) + + && + + (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) + + && + + (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); + + exit_code_for_galaxy=\$?; + cat $temp_stderr 2>&1; + (exit \$exit_code_for_galaxy) +]]> + </command> + <inputs> + <param format="par" name="input_par" type="data" label="Identification Parameters file" + help="Select PAR file from history"/> + + <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" + help="Select appropriate MGF dataset(s) from history" /> + + <!-- Search Engine Selection --> + <section name="search_engines_options" expanded="true" title="Search Engine Options"> + <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> + <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> + <option value="X!Tandem" selected="True">X!Tandem</option> + <option value="MSGF" selected="True">MS-GF+</option> + <option value="OMSSA" selected="True">OMSSA</option> + <option value="Comet">Comet</option> + <option value="Tide">Tide</option> + <option value="MyriMatch">MyriMatch</option> + <option value="MS_Amanda">MS_Amanda</option> + <!-- Windows only + <option value="Andromeda">Andromeda</option> + --> + <!-- New with version 3.0 + --> + <!--working in tests + --> + <option value="DirecTag">DirecTag</option> + <option value="Novor">Novor (Select for non-commercial use only)</option> + <validator type="no_options" message="Please select at least one output file" /> + </param> + </section> + + <conditional name="searchgui_advanced"> + <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> + <option value="basic" selected="True">Default</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" + help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> + <option value="0">no correction</option> + <option value="1" selected="True">rename spectra</option> + <option value="2">delete spectra</option> + </param> + + <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" + label="Add missing spectrum titles" help="(-missing_titles)"/> + + <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" + help="Choose a smaller value if you are running on a machine with limited memory"/> + + <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" + help="Choose a smaller value if you are running on a machine with limited memory"/> + </when> + </conditional> + + </inputs> + <outputs> + <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + + <!-- Test that specifying non-default search engines works --> + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_par" value="Identification_Parameters_specific.par"/> + <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> + <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> + </test> + <!-- Test that search works with MSAmanda --> + <test> + <param name="peak_lists" value="searchgui_smallspectra.mgf"/> + <param name="input_par" value="Identification_Parameters_default.par"/> + <param name="engines" value="MS_Amanda"/> + <output name="output" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + </test> + + </tests> + <help> +**What it does** + +Runs multiple search engines on any number of MGF peak lists using the SearchGUI. + +Default: X! Tandem, OMSSA and MS-GF+ are executed. + +Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. + + </help> + <expand macro="citations" /> +</tool>