<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 
	    $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="Synapt.QTOF.RP" help="protocolName"/>
	
	<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" />
	<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")
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 ${on_string} - metaMS LOG" hidden="True"/>
	<data name="htmlReportFile" format="html" label="${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. 
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
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>