<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>