Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 2:fb591fc7241c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Improved some datatype handling
author galaxyp
date Thu, 20 Jun 2013 11:02:36 -0400
parents 0578e296cab4
children 39416af5d0bc
comparison
equal deleted inserted replaced
1:7a74818e0eeb 2:fb591fc7241c
2 <!-- TODO: Set defaults for weights correctly --> 2 <!-- TODO: Set defaults for weights correctly -->
3 <description> 3 <description>
4 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. 4 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
5 </description> 5 </description>
6 <command> 6 <command>
7 #from datetime import datetime
8 #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")
9 #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
7 mkdir spectra; 10 mkdir spectra;
8 mkdir output; 11 mkdir output;
9 mkdir output_reports; 12 mkdir output_reports;
10 cwd=`pwd`; 13 cwd=`pwd`;
11 #for $mgf in $peak_lists: 14 #for $mgf in $peak_lists:
43 -estimate_charge ${advanced.omssa.estimate_charge} \ 46 -estimate_charge ${advanced.omssa.estimate_charge} \
44 #end if 47 #end if
45 #end if 48 #end if
46 -db $input_database; 49 -db $input_database;
47 PeptideShakerCLI \ 50 PeptideShakerCLI \
48 -experiment 'Galaxy Experiment' \ 51 -experiment '$exp_str' \
49 -sample 'Sample' \ 52 -sample '$samp_str' \
50 -replicate 1 \ 53 -replicate 1 \
51 -spectrum_files \$cwd/spectra \ 54 -spectrum_files \$cwd/spectra \
52 -identification_files \$cwd/output \ 55 -identification_files \$cwd/output \
53 -search_params \$cwd/output/SearchGUI.parameters \ 56 -search_params \$cwd/output/SearchGUI.parameters \
54 -out_txt_1 \$cwd/output_reports \ 57 -out_txt_1 \$cwd/output_reports \
208 <requirement type="package">searchgui</requirement> 211 <requirement type="package">searchgui</requirement>
209 </requirements> 212 </requirements>
210 <help> 213 <help>
211 **What it does** 214 **What it does**
212 215
216 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.
217
213 ------ 218 ------
214 219
215 **Citation** 220 **Citation**
216 221
217 For the underlying tool, please cite `TODO` 222 For the underlying tool, please cite `TODO`
218 223
219 If you use this tool in Galaxy, please cite TODO 224 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
220 </help> 225 </help>
221 </tool> 226 </tool>