# HG changeset patch
# User galaxyp
# Date 1374247978 14400
# Node ID 6521f577059f2075df1798a0e2023844a58ad2ad
# Parent 8d2702c96689fdae3d9cc4c47d48e8006b85656f
Uploaded
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
@@ -1,3 +1,231 @@
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+ Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
+
+
+ #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
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+ PeptideShaker
+ SearchGUI
+
+
+**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 results.
+
+------
+
+**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
+
+