| Previous changeset 13:6521f577059f (2013-07-19) Next changeset 15:d90e25c7b492 (2013-09-16) |
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peptide_shaker.xml |
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| diff -r 6521f577059f -r db6cc184146c peptide_shaker.xml --- a/peptide_shaker.xml Fri Jul 19 11:32:58 2013 -0400 +++ b/peptide_shaker.xml Fri Jul 19 11:39:19 2013 -0400 |
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| b'@@ -226,229 +226,3 @@\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- <!-- TODO: Set defaults for weights correctly -->\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"/>\n- <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />\n- <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">\n- <option value="1">Parts per million (ppm)</option>\n- <option value="0">Daltons</option>\n- </param> \n- <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"'..b'olean" truevalue="1" falsevalue="0" checked="false"/>\n- <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n- </when>\n- </conditional>\n- </when>\n- </conditional>\n- <conditional name="processing_options">\n- <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />\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- <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->\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" />\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 result via PeptideShaker.\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' |