Mercurial > repos > galaxyp > peptideshaker
changeset 14:db6cc184146c draft
Uploaded
author | galaxyp |
---|---|
date | Fri, 19 Jul 2013 11:39:19 -0400 |
parents | 6521f577059f |
children | d90e25c7b492 |
files | peptide_shaker.xml |
diffstat | 1 files changed, 0 insertions(+), 226 deletions(-) [+] |
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--- a/peptide_shaker.xml Fri Jul 19 11:32:58 2013 -0400 +++ b/peptide_shaker.xml Fri Jul 19 11:39:19 2013 -0400 @@ -226,229 +226,3 @@ If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker </help> </tool> -<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> - <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'; - #end for - SearchCLI \ - -spectrum_files \$cwd/spectra \ - -output_folder \$cwd/output \ - -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 $fixed_mods_str - -fixed_mods "$fixed_mods_str" \ - #end if - #if $variable_mods_str - -variable_mods "$variable_mods_str" \ - #end if - -mc $missed_cleavages \ - #if $advanced.specify: - -xtandem $advanced.xtandem \ - #if $advanced.omssa.run_omssa - #set $omssa = 1 - #else - #set $omssa = 0 - #end if - -omssa $omssa \ - #if $omssa == 1 - -hitlist_length ${advanced.omssa.hitlist_length} \ - -remove_prec ${advanced.omssa.remove_precursor} \ - -scale_prec ${advanced.omssa.scale_precursor} \ - -estimate_charge ${advanced.omssa.estimate_charge} \ - #end if - #end if - -db $input_database; - PeptideShakerCLI \ - -experiment '$exp_str' \ - -sample '$samp_str' \ - -replicate 1 \ - -spectrum_files \$cwd/spectra \ - -identification_files \$cwd/output \ - -search_params \$cwd/output/SearchGUI.parameters \ - -out_txt_1 \$cwd/output_reports \ - #if $processing_options.specify - -protein_FDR ${processing_options.protein_fdr} \ - -peptide_FDR ${processing_options.peptide_fdr} \ - -psm_FDR ${processing_options.psm_fdr} \ - -psm_FLR ${processing_options.psm_flr} \ - #if str($processing_options.a_score.use) == "1" - #set $a_score = 1 - #else - #set $a_score = 0 - #end if - -a_score $a_score \ - #if str($a_score) == "1" - -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \ - #end if - #end if - #if $filtering_options.specify - -min_peptide_length ${filtering_options.min_peptide_length} \ - -max_peptide_length ${filtering_options.max_peptide_length} \ - -max_precursor_error ${filtering_options.max_precursor_error} \ - -max_precursor_error_type ${filtering_options.max_precursor_error_type} \ - -max_xtandem_e ${filtering_options.max_xtandem_e} \ - -max_omssa_e ${filtering_options.max_omssa_e} \ - -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \ - #end if - -out \$cwd/output.cps ; - mv output_reports/*peptides.txt peptides.txt ; - mv output_reports/*psms.txt psms.txt ; - mv output_reports/*proteins.txt proteins.txt - </command> - <stdio> - <exit_code range="1:" level="fatal" description="Job Failed" /> - </stdio> - <inputs> - <param format="fasta" name="input_database" type="data" label="Protein Database"/> - <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" /> - <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"> - <option value="1">Parts per million (ppm)</option> - <option value="0">Daltons</option> - </param> - <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" /> - <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" /> - <param name="enzyme" type="select" label="Enzyme"> - <option value="Trypsin">Trypsin</option> - <option value="Arg-C">Arg-C</option> - <option value="CNBr">CNBr</option> - <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> - <option value="Formic Acid">Formic Acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-C, no P rule">Lys-C, no P rule</option> - <option value="Pepsin A">Pepsin A</option> - <option value="Trypsin + CNBr">Trypsin + CNBr</option> - <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> - <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="whole protein">whole protein</option> - <option value="Asp-N">Asp-N</option> - <option value="Glu-C">Glu-C</option> - <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> - <option value="Top-Down">Top-Down</option> - <option value="Semi-Tryptic">Semi-Tryptic</option> - <option value="No enzyme">No enzyme</option> - <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> - <option value="Asp-N (DE)">Asp-N (DE)</option> - <option value="Glu-C (DE)">Glu-C (DE)</option> - <option value="Lys-N (K)">Lys-N (K)</option> - <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> - <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> - <option value="Semi-Glu-C">Semi-Glu-C</option> - </param> - <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" /> - <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <param name="variable_modifications" type="select" label="Variable Modification" multiple="true"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <param name="min_charge" label="Minimum Charge" value="2" type="integer" /> - <param name="max_charge" label="Maximum Charge" value="4" type="integer" /> - <param name="forward_ion" label="Forward Ion" type="select"> - <option value="a">a</option> - <option value="b" selected="true">b</option> - <option value="c">c</option> - </param> - <param name="reverse_ion" label="Reverse Ion" type="select"> - <option value="x">x</option> - <option value="y" selected="true">y</option> - <option value="z">z</option> - </param> - <conditional name="advanced"> - <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <conditional name="omssa"> - <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <when value="0" /> - <when value="1"> - <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> - <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> - <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> - <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - </when> - </conditional> - </when> - </conditional> - <conditional name="processing_options"> - <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> - <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> - <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> - <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" /> - <conditional name="a_score"> - <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <when value="0" /> - <when value="1"> - <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> - </when> - </conditional> - <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> - </when> - </conditional> - <conditional name="filtering_options"> - <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> - <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> - <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> - <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> - <option value="0">ppm</option> - <option value="1">Daltons</option> - </param> - <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" /> - <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" /> - <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" /> - <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" /> - <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" /> - <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" /> - </outputs> - <requirements> - <requirement type="package" version="0.20.1">PeptideShaker</requirement> - <requirement type="package" version="1.14.1">SearchGUI</requirement> - </requirements> - <help> -**What it does** - -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. - ------- - -**Citation** - -For the underlying tool, please cite `TODO` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker - </help> -</tool>