Mercurial > repos > galaxyp > peptideshaker
diff searchgui.xml @ 18:ffed32e397cb draft
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 11 Jan 2017 13:06:06 -0500 |
| parents | 2f8e9d0351a8 |
| children | ef4ac2d49ff0 |
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--- a/searchgui.xml Fri Jun 10 09:57:31 2016 -0400 +++ b/searchgui.xml Wed Jan 11 13:06:06 2017 -0500 @@ -7,7 +7,9 @@ </macros> <requirements> <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <!-- <environment_variable name="LC_ALL" action="set_to">C</environment_variable> + --> </requirements> <expand macro="stdio" /> <command> @@ -16,21 +18,25 @@ #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 $bin_dir = "bin" mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=\$cwd; + ## echo the search engines to run + echo "$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; - cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; - tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; - #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; + #set $encoded_id = $__app__.security.encode_id($mgf.id) + echo "Spectrums:${mgf.display_name}(API:${encoded_id}) "; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta; @@ -40,7 +46,7 @@ ########################################### #if $create_decoy: echo "Creating decoy database."; - java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && + searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy && 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; @@ -49,8 +55,8 @@ ##################################################### ## generate IdentificationParameters for SearchGUI ## ##################################################### - - (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI + (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + --exec_dir="\$cwd/${bin_dir}" -out SEARCHGUI_IdentificationParameters.par @GENERAL_PARAMETERS@ @@ -196,6 +202,7 @@ -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} -andromeda_max_psms ${andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode} #end if *# @@ -245,15 +252,16 @@ #if $comet.comet_spectrum.comet_spectrum_selector == "yes" -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} - -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec} + + -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec} - #if $comet.comet_spectrum.comet_remove_prec == "1" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - #if $comet.comet_spectrum.comet_remove_prec == "2" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower} @@ -279,13 +287,44 @@ #end if #end if + #if $directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${directtag.directag_tic_cutoff} + -directag_max_peak_count ${directtag.directag_max_peak_count} + -directag_intensity_classes ${directtag.directag_intensity_classes} + -directag_adjust_precursor ${directtag.directag_adjust_precursor} + -directag_min_adjustment ${directtag.directag_min_adjustment} + -directag_max_adjustment ${directtag.directag_max_adjustment} + -directag_adjustment_step ${directtag.directag_adjustment_step} + -directag_charge_states ${directtag.directag_charge_states} + #if str($directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${directtag.directag_output_suffix} + #end if + -directag_ms_charge_state ${directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${directtag.directag_duplicate_spectra} + -directag_deisotoping ${directtag.directag_deisotoping} + -directag_isotope_tolerance ${directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${directtag.directag_complement_tolerance} + -directag_tag_length ${directtag.directag_tag_length} + -directag_max_var_mods ${directtag.directag_max_var_mods} + -directag_max_tag_count ${directtag.directag_max_tag_count} + -directag_intensity_weight ${directtag.directag_intensity_weight} + -directag_fidelity_weight ${directtag.directag_fidelity_weight} + -directag_complement_weight ${directtag.directag_complement_weight} + #end if + + #if $novor.novor_advanced == "yes" + -novor_fragmentation ${novor.novor_fragmentation} + -novor_mass_analyzer ${novor.novor_mass_analyzer} + #end if + 2> $temp_stderr) && ################ ## Search CLI ## ################ - (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI + (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI + --exec_dir="\$cwd/${bin_dir}" -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output @@ -355,6 +394,18 @@ -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 @@ -396,19 +447,26 @@ <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> - <!-- Not working in tests - <option value="MyriMatch">MyriMatch</option> - <option value="MS_Amanda">MS_Amanda</option> - --> + <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> <!-- Not working in tests + --> <option value="Tide">Tide</option> + <!-- Not working in tests --> + <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> @@ -439,7 +497,7 @@ <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> + </when> </conditional> @@ -470,7 +528,7 @@ <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_evalue" help="Highest value for recorded peptides" - label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" /> + label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> <param name="xtandem_output_proteins" help="Controls output of protein sequences" label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_sequences" help="Controls output of sequence information" @@ -867,6 +925,7 @@ <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" /> </when> </conditional> --> @@ -891,20 +950,22 @@ label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> <param name="comet_min_peak_int" type="float" value="0.0" label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> - <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> - <option value="0" selected="True" >off</option> - <option value="1">on</option> - <option value="2">as expected for ETD/ECD spectra</option> - </param> - <when value="0" /> - <when value="1"> - <param name="comet_remove_prec_tol" type="float" value="1.5" - label="Comet: Remove Precursor Tolerance" /> - </when> - <when value="2"> - <param name="comet_remove_prec_tol" type="float" value="1.5" - label="Comet: Remove Precursor Tolerance" /> - </when> + <conditional name="comet_prec"> + <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> + <option value="0" selected="True" >off</option> + <option value="1">on</option> + <option value="2">as expected for ETD/ECD spectra</option> + </param> + <when value="0" /> + <when value="1"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + <when value="2"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + </conditional> <param name="comet_clear_mz_range_lower" type="float" value="0.0" label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> <param name="comet_clear_mz_range_upper" type="float" value="0.0" @@ -964,6 +1025,59 @@ </conditional> </when> </conditional> + <conditional name="directtag"> + <param name="directtag_advanced" type="select" label="DirectTag Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/> + <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/> + <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/> + <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/> + <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/> + <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/> + <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/> + <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/> + <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/> + <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/> + <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/> + <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping"> + <option value="0" selected="true">no deisotoping</option> + <option value="1">precursor only</option> + <option value="2">precursor and candidate</option> + </param> + <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/> + <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/> + <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/> + <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/> + <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/> + <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/> + <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/> + <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/> + </when> + </conditional> + + <conditional name="novor"> + <param name="novor_advanced" type="select" label="Novor Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> + <option value="HCD" selected="True">HCD</option> + <option value="CID">CID</option> + </param> + <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> + <option value="FT" selected="True">FT</option> + <option value="Trap" >Trap</option> + <option value="TOF" >TOF</option> + </param> + </when> + </conditional> + </inputs> <outputs> <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />