diff metams_lcms_annotate.xml @ 41:e67149fbff20

small changes/improvements; new metams and xcms tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metams_lcms_annotate.xml	Thu Nov 06 16:14:44 2014 +0100
@@ -0,0 +1,136 @@
+<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.3">
+	<description> Runs metaMS process for LC/MS feature grouping and annotation</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		metaMS_cmd_interface.r 
+	    $constructed_db
+	    $data_files
+	    $customMetaMSsettings
+	    $outputFile 
+	    $outputLog
+	    $xsetOut
+	    $htmlReportFile
+	    $htmlReportFile.files_path
+	</command>
+<inputs>
+	<param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards
+	against a manually validated reference table which contains the key analytical information for each standard." 
+      		 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
+	
+	<param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDFs)" help=".zip file containing the CDF files of the new measurements"/>
+	
+	
+	
+	<param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
+	
+	<param name="method" type="select" size="30" label="PEAK PICKING method =====================================================">
+		<option value="matchedFilter" selected="true">matchedFilter</option>
+	</param>
+	<param name="step" type="float" size="10" value="0.05" label="step" help="step"/>
+	<param name="fwhm" type="integer" size="10" value="20" label="fwhm" help="fwhm" />
+	<param name="snthresh" type="integer" size="10" value="4" label="snthresh" help="snthresh" />
+	<param name="max" type="integer" size="10" value="50" label="max" help="max" />
+	
+	<param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" help="min.class.fraction"/>
+	<param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" help="min.class.size" />
+	<param name="mzwid" type="float" size="10" value="0.1" label="mzwid" help="mzwid"/>
+	<param name="bws" type="text" size="10" value="30,10" label="bws" help="bws"/>
+	<param name="missingratio" type="float" size="10" value="0.2" label="missingratio" help="missingratio"/>
+	<param name="extraratio" type="float" size="10" value="0.1" label="extraratio" help="extraratio"/>
+	<param name="retcormethod" type="select" size="30" label="retcormethod" help="retcormethod">
+		<option value="linear" selected="true">linear</option>
+	</param>
+	<param name="retcorfamily" type="select" size="30" label="retcorfamily" help="retcorfamily">
+		<option value="symmetric" selected="true">symmetric</option>
+	</param>
+	<param name="fillPeaks" type="select" size="30" label="fillPeaks" help="fillPeaks">
+		<option value="TRUE" selected="true">Yes</option>
+		<option value="FALSE">No</option>
+	</param>
+	<param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" help="perfwhm"/>
+	<param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" help="cor_eic_th" />
+	<param name="ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
+	<param name="rtdiff" type="float" size="10" value="1.5" label="MATCH2DB rtdiff =====================================================" help="rtdiff"/>
+	<param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" />
+	<param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" />
+	<param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
+	<param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" />
+	
+</inputs>
+<configfiles>
+
+<configfile name="customMetaMSsettings">## start comment
+		## metaMS process settings
+		customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
+                            chrom = "LC",
+                            PeakPicking = list(
+                              method = "${method}",
+                              step = ${step},
+                              fwhm = ${fwhm},
+                              snthresh = ${snthresh},
+                              max = ${max}),
+                            Alignment = list(
+                              min.class.fraction = ${min_class_fraction},
+                              min.class.size = ${min_class_size},
+                              mzwid = ${mzwid},
+                              bws = c(${bws}),
+                              missingratio = ${missingratio},
+                              extraratio = ${extraratio},
+                              retcormethod = "${retcormethod}",
+                              retcorfamily = "${retcorfamily}",            
+                              fillPeaks = ${fillPeaks}),
+                            CAMERA = list(
+                              perfwhm = ${perfwhm},
+                              cor_eic_th = ${cor_eic_th},
+                              ppm= ${ppm}))
+metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
+            rtdiff = ${rtdiff},
+            rtval = ${rtval},
+            mzdiff = ${mzdiff},
+            ppm = ${match2DB_ppm},
+            minfeat = ${minfeat})</configfile>
+
+</configfiles>
+
+<outputs>
+	<data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
+	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG"/>
+	<data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - metaMS xcmsSet (RDATA)"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
+<help>
+
+.. class:: infomark
+  
+Runs metaMS process for LC/MS feature grouping and annotation. Parts of the metaMS process also make use of the XCMS and CAMERA tools and algorithms.
+The figure below shows the main parts of the metaMS process. 
+
+.. image:: $PATH_TO_IMAGES/metaMS.png 
+
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Wehrens, R.; Weingart, G.; Mattivi, F. (2014). 
+metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. 
+Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. 
+doi: 10.1016/j.jchromb.2014.02.051 
+handle: http://hdl.handle.net/10449/24012
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
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