diff ms2preproc.xml @ 0:59e5d8c53c81 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms2preproc.xml	Wed Dec 19 00:27:24 2012 -0500
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+<tool id="ms2preproc" name="ms2preproc" version="0.1.0">
+  <description>preprocess and filter MS/MS spectra</description>
+
+  <command>
+    #if $window:
+    #set $window_arg = "-Z %s" % $window
+    #else
+    #set $window_arg = ""
+    #end if
+    ms2preproc --infile ${input} --outfile ${output} --informat mgf --top ${top} ${window_arg}; sed -i -e 's/,SCAN\(.*\)$/\nSCANS=\1/' ${output}
+  </command>
+
+  <inputs>
+    <param format="mgf" name="input" type="data" label="Input MGF" />
+    <param name="top" type="integer" label="Number of top peaks to keep" value="200" help="" />
+    <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)" />
+  </inputs>
+  <outputs>
+    <data format="mgf" name="output" label="ms2preproc on ${on_string}"/>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">ms2preproc</requirement>  
+  </requirements>
+
+  <help>
+**What it does**
+
+ms2preproc is a software tool to preprocess MS/MS spectra, please see the citation below for more information.
+
+**Inputs and Parameters**
+
+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.
+
+The authors of this software recommend running ms2preproc with the following settings:
+
+  Mascot: 
+    Select top 200 peaks globally. 
+
+  Sequest: 
+    Select top 6 peaks in windows of size 30 m/z.
+
+  ProteinPilot: 
+    Select top 6 peaks in windows of size 30 m/z.
+
+------
+
+**Citation**
+
+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).`
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-ms2preproc
+  </help>
+</tool>