Mercurial > repos > bgruening > peptideshaker
changeset 3:7939608a991c draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 02 May 2014 15:34:25 -0400 |
| parents | e873824c4198 |
| children | 020836ac3b8e |
| files | peptide_shaker.xml tool_dependencies.xml |
| diffstat | 2 files changed, 74 insertions(+), 38 deletions(-) [+] |
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--- a/peptide_shaker.xml Fri May 02 02:35:17 2014 -0400 +++ b/peptide_shaker.xml Fri May 02 15:34:25 2014 -0400 @@ -1,26 +1,28 @@ <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0"> - <!-- TODO: Set defaults for weights correctly --> + <description> + Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + </description> <requirements> <requirement type="package" version="0.28.0">peptide_shaker</requirement> <requirement type="package" version="1.18.0">searchgui</requirement> - <!--<requirement type="package" version="2.2.29">blast+</requirement>--> + <requirement type="package" version="2.2.29">blast+</requirement> </requirements> - <description> - Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. - </description> + <stdio> + <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") - mkdir spectra; mkdir output; mkdir output_reports; cwd=`pwd`; #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" - ln -s '${mgf}' 'spectra/${input_name}'; + ln -s '${mgf}' '${input_name}'; #end for - ln -s ${input_database} input_database.fasta; + #ln -s "${input_database}" input_database.fasta; + cp "${input_database}" input_database.fasta; ########################################### #### Creating decoy database #### @@ -28,7 +30,9 @@ #if $create_decoy: echo "Creating decoy database."; java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy; - ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; + rm input_database.fasta; + cp input_database_concatenated_target_decoy.fasta input_database.fasta; + #ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; #end if ##################################################### @@ -41,8 +45,8 @@ -prec_tol "${precursor_ion_tol}" -frag_tol "${fragment_tol}" -enzyme "${enzyme}" - #set $fixed_mods_str = ${fixed_modifications} or '' - #set $variable_mods_str = ${variable_modifications} or '' + #set $fixed_mods_str = $fixed_modifications or '' + #set $variable_mods_str = $variable_modifications or '' #if $fixed_mods_str -fixed_mods "${fixed_mods_str}" #end if @@ -82,12 +86,12 @@ ################ java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI -temp_folder `pwd` - -spectrum_files \$cwd/spectra + -spectrum_files \$cwd -output_folder \$cwd/output -id_params SEARCHGUI_IdentificationParameters.parameters -threads "\${GALAXY_SLOTS:-12}" - -correct_titles $correct_titles + -correct_titles "${correct_titles}" -mgf_splitting "${mgf_splitting}" -mgf_spectrum_count "${mgf_spectrum_count}" @@ -101,6 +105,7 @@ #if $advanced.omssa.omssa_selector == "yes" -omssa 1 + -makeblastdb_folder \$BLAST_ROOT_DIR #else -omssa 0 #end if @@ -125,10 +130,10 @@ ######################################################### 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 - -frag_tol $fragment_tol - -enzyme '$enzyme' + -prec_ppm "${precursor_ion_tol_units}" + -prec_tol "${precursor_ion_tol}" + -frag_tol "${fragment_tol}" + -enzyme "${enzyme}" #set $fixed_mods_str = $fixed_modifications or '' #set $variable_mods_str = $variable_modifications or '' #if $fixed_mods_str @@ -153,15 +158,15 @@ -experiment '${exp_str}' -sample '${samp_str}' -replicate 1 - -spectrum_files \$cwd/spectra + -spectrum_files \$cwd -identification_files \$cwd/output -out \$cwd/peptide_shaker_output.cps -id_params PEPTIDESHAKER_IdentificationParameters.parameters ##Optional gene annotation parameter - #if "${species_type.species_type_selector}" != 'no_species_type': + #if $species_type.species_type_selector != 'no_species_type': -species_type "${species_type.species_type_selector}" - -species "{$species_type.species}" + -species "${species_type.species}" #end if ##Optional processing parameters: @@ -179,7 +184,6 @@ -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" #end if - ##Optional filtering parameters: #if $filtering_options.filtering_options_selector == "yes": -min_peptide_length "${filtering_options.min_peptide_length}" @@ -191,7 +195,6 @@ -max_mascot_e "${filtering_options.max_mascot_e}" -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" #end if - ; ################################## @@ -201,16 +204,25 @@ -temp_folder `pwd` -in \$cwd/peptide_shaker_output.cps -out_reports \$cwd/output_reports - + -reports str($outputs).split(',').remove('cps') ; - ##mv output_reports/*peptides.txt peptides.txt ; - ##mv output_reports/*psms.txt psms.txt ; - ##mv output_reports/*proteins.txt proteins.txt + #if '0' in str($outputs).split(','): + find . -name '\$cwd/output_reports/*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; + #end if + #if '1' in str($outputs).split(','): + find . -name '\$cwd/output_reports/*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \; + #end if + #if '2' in str($outputs).split(','): + find . -name '\$cwd/output_reports/*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; + #end if + #if '3' in str($outputs).split(','): + find . -name '\$cwd/output_reports/*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; + #end if + #if '4' in str($outputs).split(','): + find . -name '\$cwd/output_reports/*Top*' -exec bash -c 'mv "$0" ".txt"' {} \; + #end if </command> - <stdio> - <exit_code range="1:" level="fatal" description="Job Failed" /> - </stdio> <inputs> <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> @@ -622,12 +634,36 @@ <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> </when> </conditional> + + <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> + <option value="2" selected="True">Peptide Report</option> + <option value="3" selected="True">Protein Report</option> + <option value="1">PSM Report</option> + <option value="0">Certificate of Analysis</option> + <option value="4">Top Down Report</option> + <option value="cps">CPS file</option> + <validator type="no_options" message="Please select at least one output file." /> + </param> </inputs> <outputs> - <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="PeptideShaker CPS results for ${on_string}" /> - <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="PeptideShaker Peptide Report for ${on_string}" /> - <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="PeptideShaker Protein Report for ${on_string}" /> - <data format="tabular" name="output_psms" from_work_dir="psms.txt" label="PeptideShaker PSM Report for ${on_string}" /> + <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> + <filter>'cps' in outputs</filter> + </data> + <data format="text" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> + <filter>'0' in outputs</filter> + </data> + <data format="text" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> + <filter>'1' in outputs</filter> + </data> + <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> + <filter>'2' in outputs</filter> + </data> + <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> + <filter>'3' in outputs</filter> + </data> + <data format="tabular" name="output_top_down" from_work_dir="top_down.txt" label="${tool.name} on ${on_string}: Top Down Report"> + <filter>'4' in outputs</filter> + </data> </outputs> <help> **What it does**
--- a/tool_dependencies.xml Fri May 02 02:35:17 2014 -0400 +++ b/tool_dependencies.xml Fri May 02 15:34:25 2014 -0400 @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="searchgui" version="1.18.0"> - <repository changeset_revision="dacab27c8ed9" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ee938eef1013" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="peptide_shaker" version="0.28.0"> - <repository changeset_revision="dc40b31c1d5b" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="dc40b31c1d5b" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <!--<package name="blast+" version="2.2.29"> - <repository name="package_blast_plus_2_2_29" owner="iuc" /> - </package>--> + <package name="blast+" version="2.2.29"> + <repository changeset_revision="e78bbab7933d" name="package_blast_plus_2_2_29" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>