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Changeset 13:6521f577059f (2013-07-19)

Previous changeset 12:8d2702c96689 (2013-07-19) Next changeset 14:db6cc184146c (2013-07-19)

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modified:
peptide_shaker.xml

diff -r 8d2702c96689 -r 6521f577059f peptide_shaker.xml
--- a/peptide_shaker.xml Fri Jul 19 11:20:56 2013 -0400
+++ b/peptide_shaker.xml Fri Jul 19 11:32:58 2013 -0400

b'@@ -1,3 +1,231 @@\n+<tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">\n+ \n+ <description>\n+ Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.\n+ </description>\n+ <command>\n+ #from datetime import datetime\n+ #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s") \n+ #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")\n+ mkdir spectra;\n+ mkdir output;\n+ mkdir output_reports;\n+ cwd=`pwd`;\n+ #for $mgf in $peak_lists:\n+ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n+ ln -s \'$mgf\' \'spectra/$input_name\';\n+ #end for\n+ SearchCLI \\\n+ -spectrum_files \\$cwd/spectra \\\n+ -output_folder \\$cwd/output \\\n+ -ppm $precursor_ion_tol_units \\\n+ -prec_tol $precursor_ion_tol \\\n+ -frag_tol $fragment_tol \\\n+ -enzyme \'$enzyme\' \\\n+ #set $fixed_mods_str = $fixed_modifications or \'\'\n+ #set $variable_mods_str = $variable_modifications or \'\'\n+ #if $fixed_mods_str\n+ -fixed_mods "$fixed_mods_str" \\\n+ #end if\n+ #if $variable_mods_str\n+ -variable_mods "$variable_mods_str" \\\n+ #end if\n+ -mc $missed_cleavages \\\n+ #if $advanced.specify:\n+ -xtandem $advanced.xtandem \\\n+ #if $advanced.omssa.run_omssa\n+ #set $omssa = 1\n+ #else \n+ #set $omssa = 0\n+ #end if\n+ -omssa $omssa \\\n+ #if $omssa == 1\n+ -hitlist_length ${advanced.omssa.hitlist_length} \\\n+ -remove_prec ${advanced.omssa.remove_precursor} \\\n+ -scale_prec ${advanced.omssa.scale_precursor} \\\n+ -estimate_charge ${advanced.omssa.estimate_charge} \\\n+ #end if\n+ #end if\n+ -db $input_database;\n+ PeptideShakerCLI \\\n+ -experiment \'$exp_str\' \\\n+ -sample \'$samp_str\' \\ \n+ -replicate 1 \\\n+ -spectrum_files \\$cwd/spectra \\\n+ -identification_files \\$cwd/output \\ \n+ -search_params \\$cwd/output/SearchGUI.parameters \\\n+ -out_txt_1 \\$cwd/output_reports \\\n+ #if $processing_options.specify\n+ -protein_FDR ${processing_options.protein_fdr} \\\n+ -peptide_FDR ${processing_options.peptide_fdr} \\ \n+ -psm_FDR ${processing_options.psm_fdr} \\\n+ -psm_FLR ${processing_options.psm_flr} \\\n+ #if str($processing_options.a_score.use) == "1"\n+ #set $a_score = 1\n+ #else\n+ #set $a_score = 0\n+ #end if\n+ -a_score $a_score \\\n+ #if str($a_score) == "1"\n+ -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \\\n+ #end if\n+ #end if\n+ #if $filtering_options.specify\n+ -min_peptide_length ${filtering_options.min_peptide_length} \\\n+ -max_peptide_length ${filtering_options.max_peptide_length} \\\n+ -max_precursor_error ${filtering_options.max_precursor_error} \\\n+ -max_precursor_error_type ${filtering_options.max_precursor_error_type} \\\n+ -max_xtandem_e ${filtering_options.max_xtandem_e} \\\n+ -max_omssa_e ${filtering_options.max_omssa_e} \\\n+ -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \\\n+ #end if\n+ -out \\$cwd/output.cps ; \n+ mv output_reports/*peptides.txt peptides.txt ;\n+ mv output_reports/*psms.txt psms.txt ;\n+ mv output_reports/*proteins.txt proteins.txt\n+ </command>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ </stdio>\n+ <inputs>\n+ <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"/>\n+ <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" />\n+ <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n+ <option value="1">P'..b'e options for post-translational modifications (PTM\xe2\x80\x99s). See this link_ for more details\n+\n+ .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />\n+ <when value="false" />\n+ <when value="true">\n+ <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: \'1\'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />\n+ <conditional name="a_score">\n+ <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n+ <when value="0" />\n+ <when value="1">\n+ <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />\n+ </when>\n+ </conditional>\n+ \n+ </when>\n+ </conditional> \n+ <conditional name="filtering_options">\n+ <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM\xe2\x80\x99s"/>\n+ <when value="false" />\n+ <when value="true">\n+ <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />\n+ <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />\n+ <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />\n+ <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">\n+ <option value="0">ppm</option>\n+ <option value="1">Daltons</option>\n+ </param>\n+ <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />\n+ <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />\n+ <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />\n+ <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />\n+ <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />\n+ <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />\n+ </outputs>\n+ <requirements>\n+ <requirement type="package" version="0.20.1">PeptideShaker</requirement>\n+ <requirement type="package" version="1.14.1">SearchGUI</requirement>\n+ </requirements>\n+ <help>\n+**What it does**\n+\n+Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `TODO`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker\n+ </help>\n+</tool>\n <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">\n \n <description>\n'