--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS/metams_lcms_annotate.xml	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,121 @@
+<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.4">
+	<description> Runs metaMS process for LC/MS feature annotation</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		metaMS_cmd_annotate.r 
+	    $constructed_db
+	    $xsetData
+	    $customMetaMSsettings
+	    $outputFile 
+	    #if $mzTol.mzTolType == "fixed"  
+			0
+		#else
+            "$mzTol.mass_error_function"
+		#end if
+	    $htmlReportFile
+	    $htmlReportFile.files_path
+	    $outputLog
+	</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="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/>
+	
+	<param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP" 
+		help="Choose a name to give for the specific settings in the parameters below"/>
+	
+	<param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="(Annotation) Allowed rt difference (in minutes)"/>
+	
+	<conditional name="mzTol">
+		<param name="mzTolType" type="select" size="30" label="(Annotation) m/z tolerance type">
+			<option value="fixed" selected="true">Fixed tolerance</option>
+			<option value="adaptive" >Adaptive tolerance</option>
+		</param>
+		<when value="fixed">
+			<param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="(Annotation) Fixed mass tolerance" />
+		</when>
+		<when value="adaptive">
+			<param name="ppm" type="float" size="10" value="5.0" label="ppm" help="(Annotation) Tolerance in ppm" />
+			<param name="mass_error_function" type="text" area="true" size="3x70" label="(Annotation) Mass error function"/>
+		</when>
+	</conditional>
+
+	<param name="rtval" type="float" size="10" value="0.1" label="(max)rtval" help="(Validation) Group items are clustered once more with hierarchical clustering ('complete' method)
+	          based on their rt distances. Here one can specify the rt threshold for removing the items that have too diverging rt (the ones with rt difference 
+	          larger than rtval). " />
+	<param name="minfeat" type="integer" size="10" value="2" label="minfeat" 
+	           help="(Validation) Threshold for the minimum number of features a 
+	           cluster/group should have (after rtval filtering above). Other clusters/groups are filtered out." />
+	
+</inputs>
+<configfiles>
+
+<configfile name="customMetaMSsettings">## start comment
+		## metaMS process settings
+		customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
+                            chrom = "LC")
+metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
+            rtdiff = ${rtdiff},
+            rtval = ${rtval},
+		#if $mzTol.mzTolType == "fixed"  
+			mzdiff = ${mzTol.mzdiff},
+		#else
+            ppm = ${mzTol.ppm},
+		#end if
+            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 ${on_string} - metaMS LOG" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${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 annotation based on matching to an existing 'standards' DB.  
+The figure below shows the main parts of this metaMS process.
+
+.. image:: $PATH_TO_IMAGES/metaMS_annotate.png 
+
+
+.. class:: infomark
+
+The implemented annotation strategy can be broken down in the following steps:
+
+1. *Feature wise Annotation:* Each feature detected by runLC is matched against the database. If
+the mass error function is provided, the appropriate m/z tolerance is calculated, otherwise a fixed
+tolerance is used (mzdiff). The retention time tolerance is fixed and should be selected on the
+bases of the characteristics of each chromatographic method (rtdiff). Multiple annotations - i.e.
+features which are associated to more than one compound - are possible. This outcome does not
+indicate a problem per se, but is an inherent drawback of co-elution.
+
+2. *Annotation Validation:* The annotated features are organized in 'pseudospectra' collecting all
+the experimental features which are assigned to a specific compound. A specific annotation is
+confirmed only if more than minfeat features which differ in retention time less than rtval are
+present in a pseudospectrum. As a general rule rtval should be narrower than rtdiff. The
+latter, indeed, accounts for shifts in retention time between the injection of the standards and the
+metabolomics experiment under investigation. This time can be rather long, considering that the
+standards are not commonly re-analyzed each time. On the other hand, rtval represents the shift
+between the ions of the same compound within the same batch of injections and therefore it has
+only to account for the smaller shifts occurring during peak picking and alignment.
+
+
+  </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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