diff metams_lcms_annotate.xml @ 49:f772a5caa86a

Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.

--- a/metams_lcms_annotate.xml	Wed Nov 19 15:11:45 2014 +0100
+++ b/metams_lcms_annotate.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -1,58 +1,28 @@
-<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>
+<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_interface.r 
+		metaMS_cmd_annotate.r 
 	    $constructed_db
-	    $data_files
+	    $xsetData
 	    $customMetaMSsettings
 	    $outputFile 
-	    $outputLog
-	    $xsetOut
 	    $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="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="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="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="rtdiff" type="float" size="10" value="1.5" label="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" />
@@ -64,27 +34,7 @@
 <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}))
+                            chrom = "LC")
 metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
             rtdiff = ${rtdiff},
             rtval = ${rtval},
@@ -96,8 +46,7 @@
 
 <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 ${on_string} - metaMS xcmsSet (RDATA)"/>
+	<data name="outputLog" format="txt" label="${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>
@@ -109,12 +58,17 @@
 
 .. 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. 
+Runs metaMS process for LC/MS feature annotation. 
+The figure below shows the main parts of the metaMS process.
+This tool related to the last step of this process. 
 
 .. image:: $PATH_TO_IMAGES/metaMS.png 
 
 
+From CAMERA documentation: 
+
+.. image:: $PATH_TO_IMAGES/CAMERA_results.png 
+
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please