Mercurial > repos > bgruening > peptideshaker
changeset 12:b9f2cedab007 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 09 May 2014 04:02:11 -0400 |
| parents | e5bdaa2ac9c7 |
| children | 7a76958125be |
| files | peptide_shaker.xml |
| diffstat | 1 files changed, 86 insertions(+), 17 deletions(-) [+] |
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--- a/peptide_shaker.xml Wed May 07 00:47:14 2014 -0400 +++ b/peptide_shaker.xml Fri May 09 04:02:11 2014 -0400 @@ -11,9 +11,12 @@ <exit_code range="1:" level="fatal" description="Job Failed" /> </stdio> <command> + #from datetime import datetime #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 $temp_stderr = 'macs2_stderr' + mkdir output; mkdir output_reports; cwd=`pwd`; @@ -39,7 +42,7 @@ ## generate IdentificationParameters for SearchGUI ## ##################################################### - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI + (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI -out SEARCHGUI_IdentificationParameters.parameters -prec_ppm "${precursor_ion_tol_units}" -prec_tol "${precursor_ion_tol}" @@ -62,8 +65,23 @@ #if $advanced.advanced_type_selector == "advanced": - ##if $advanced.xtandem.xtandem_selector == "yes" - ##end if + #if $advanced.xtandem.xtandem_selector == "yes" + + -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} + + #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" + -xtandem_refine 1 + -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} + #end if + #end if #if $advanced.omssa.omssa_selector == "yes" -omssa_hitlist_length ${advanced.omssa.hitlist_length} @@ -72,19 +90,26 @@ -omssa_estimate_charge ${advanced.omssa.estimate_charge} #end if - ##if $advanced.msgf.msgf_selector == "yes" - ##end if + #if $advanced.msgf.msgf_selector == "yes" + -msgf_decoy ${advanced.msgf.msgf_decoy} + -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} + -msgf_termini ${advanced.msgf.msgf_termini} + -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} + #end if ##if $advanced.ms_amanda.ms_amanda_selector == "yes" ##end if #end if - ; + + 2> $temp_stderr) + && ################ ## Search CLI ## ################ - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output @@ -128,12 +153,13 @@ #end if #end if - ; + 2>> $temp_stderr) + && ######################################################### ## generate IdentificationParameters for PeptideShaker ## ######################################################### - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI -out PEPTIDESHAKER_IdentificationParameters.parameters -prec_ppm "${precursor_ion_tol_units}" -prec_tol "${precursor_ion_tol}" @@ -153,12 +179,14 @@ -fi $forward_ion -ri $reverse_ion -db input_database.fasta - ; + + 2>> $temp_stderr) + && ###################### ## PeptideShakerCLI ## ###################### - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` -experiment '${exp_str}' -sample '${samp_str}' @@ -200,12 +228,14 @@ -max_mascot_e "${filtering_options.max_mascot_e}" -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" #end if - ; + + 2>> $temp_stderr) + && ################################## ## PeptideShaker Report options ## ################################## - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI -temp_folder `pwd` -in \$cwd/peptide_shaker_output.cps -out_reports \$cwd/output_reports @@ -216,7 +246,9 @@ #else: -reports #echo str($outputs)# #end if - ; + + 2>> $temp_stderr) + && #if '0' in str($outputs).split(','): find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; @@ -239,8 +271,10 @@ ; #end if - ## the following line is needed. Otherwise, Galaxy will strip away the ';' - echo 'Finished!'; + exit_code_for_galaxy=\$?; + cat $temp_stderr 2>&1; + (exit \$exit_code_for_galaxy) + </command> <inputs> <param format="fasta" name="input_database" type="data" label="Protein Database" @@ -567,7 +601,30 @@ </param> <when value="no" /> <when value="yes"> - </when> + + + <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/> + <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/> + <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/> + <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/> + + + <conditional name="xtandem_refine"><!-- -xtandem_refine --> + <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> + <option value="no" selected="True">Don't refine</option> + <option value="yes" >Use refinement</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/> + <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/> + <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/> + </when> + </conditional> + </when> </conditional> <conditional name="omssa"> @@ -591,6 +648,15 @@ </param> <when value="no" /> <when value="yes"> + <param name="msgf_decoy" label="MS-GF+: Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> + <param name="msgf_min_pep_length" label="MS-GF+: Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" label="MS-GF+: Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" label="MS-GF+: Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2"> + <option value="0">0 (ie non-specific cleavage)</option> + <option value="1">1 (ie semi-tryptic cleavage)</option> + <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> + </param> + <param name="msgf_num_ptms" label="MS-GF+: Max PTMs per peptide" type="integer" value="2"/> </when> </conditional> @@ -694,6 +760,9 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="advanced_type_selector" value="advanced"/> + <param name="species_type_selector" value="no_species_type"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="no"/> <param name="xtandem_selector" value="yes"/> <param name="omssa_selector" value="no"/> <param name="msgf_selector" value="yes"/>