Mercurial > repos > galaxyp > ms2preproc
comparison ms2preproc.xml @ 0:59e5d8c53c81 draft
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| author | galaxyp |
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| date | Wed, 19 Dec 2012 00:27:24 -0500 |
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| -1:000000000000 | 0:59e5d8c53c81 |
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| 1 <tool id="ms2preproc" name="ms2preproc" version="0.1.0"> | |
| 2 <description>preprocess and filter MS/MS spectra</description> | |
| 3 | |
| 4 <command> | |
| 5 #if $window: | |
| 6 #set $window_arg = "-Z %s" % $window | |
| 7 #else | |
| 8 #set $window_arg = "" | |
| 9 #end if | |
| 10 ms2preproc --infile ${input} --outfile ${output} --informat mgf --top ${top} ${window_arg}; sed -i -e 's/,SCAN\(.*\)$/\nSCANS=\1/' ${output} | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param format="mgf" name="input" type="data" label="Input MGF" /> | |
| 15 <param name="top" type="integer" label="Number of top peaks to keep" value="200" help="" /> | |
| 16 <param name="window" type="float" label="m/z Window" value="" optional="true" help="m/z Windows (+/-Z) around high-intensity peaks in which the number specified above are selected. (Optional)" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="mgf" name="output" label="ms2preproc on ${on_string}"/> | |
| 20 </outputs> | |
| 21 | |
| 22 <requirements> | |
| 23 <requirement type="package">ms2preproc</requirement> | |
| 24 </requirements> | |
| 25 | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 29 ms2preproc is a software tool to preprocess MS/MS spectra, please see the citation below for more information. | |
| 30 | |
| 31 **Inputs and Parameters** | |
| 32 | |
| 33 ms2preproc is very specific about the formatting of the MGF file it parses. Therefore it is recommended that the MGF Formatter tool is used to create a MGF file specifically for ms2preproc prior to the use of this tool. | |
| 34 | |
| 35 The authors of this software recommend running ms2preproc with the following settings: | |
| 36 | |
| 37 Mascot: | |
| 38 Select top 200 peaks globally. | |
| 39 | |
| 40 Sequest: | |
| 41 Select top 6 peaks in windows of size 30 m/z. | |
| 42 | |
| 43 ProteinPilot: | |
| 44 Select top 6 peaks in windows of size 30 m/z. | |
| 45 | |
| 46 ------ | |
| 47 | |
| 48 **Citation** | |
| 49 | |
| 50 For the underlying tool, please cite `Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H. When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification, Proteomics (2009).` | |
| 51 | |
| 52 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-ms2preproc | |
| 53 </help> | |
| 54 </tool> |