<tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs"  version="0.0.4">
	<description> Extracts alignment EICs from feature alignment data</description>
	<requirements>
		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
	</requirements>	
	<command interpreter="Rscript">
		xcms_get_alignment_eic.r 
	    $xsetData
		$rtStart
		$rtEnd
		$minNrSamples
		"$sampleNames" 
		$htmlReportFile
		$htmlReportFile.files_path
		$outLogFile
	</command>
<inputs>
	
	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
	
	
	<param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
	<param name="rtEnd" type="integer" value="" size="10"  label="RT end" help="End of Retention Time region to plot" />
	
	<param name="minNrSamples" type="integer" size="10" value="10" label="Minimum number of samples in which aligned feature should be found" help="Can also read this as: Minimum 
	number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together." />
	
	<param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names" 
	value="sampleName1,sampleName2,etc"
	help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
	to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
		<sanitizer>
			<!-- this translates from line-separated to comma separated list -->
			<valid/>
			<mapping initial="none">
		    	<add source="&#10;" target=","/>
		    	<add source="&#13;" target=""/>
 			</mapping>
		</sanitizer>	
	</param>
	
	
</inputs>
<outputs>
	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
</outputs>
<tests>
	<test>
	</test>
</tests>
<help>

.. class:: infomark
 
This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method. 
It produces a HTML report showing the EIC plots and the mass list of each alignment. The figure below shows an example of such an EIC plot, showing also the difference between 
two classes, with extra alignment information beneath it.
 
.. image:: $PATH_TO_IMAGES/diffreport.png 

Alignment id: 1709. m/z list of peaks in alignment:
614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469


  </help>
  <citations>
        <citation type="doi">10.1021/ac051437y</citation> <!-- example 
        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
        -->
   </citations>
</tool>