view xcms_get_mass_eic.xml @ 60:35f506f30ae4

fixed small rule in pdfread, and other small enhancements

<tool id="xcms_get_mass_eic" name="XCMS Get EICs"  version="0.0.4">
	<description> Extracts EICs for a given list of masses</description>
	<requirements>
		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
	</requirements>	
	<command interpreter="Rscript">
		xcms_get_mass_eic.r 
	    $xsetData
		$rtStart
		$rtEnd
		#if $massParameters.massParametersType == "window"
			$massParameters.mzStart 
			$massParameters.mzEnd
			-1
			"."
		#else
			-1
			-1
			"$massParameters.mzList" 
			$massParameters.mzTolPpm
		#end if  
		"$sampleNames" 
		$combineSamples
		$rtPlotMode
		$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" />
	
	<conditional name="massParameters">
		<param name="massParametersType" type="select" size="50" label="Give masses as" >
			<option value="list" selected="true">m/z list</option>
			<option value="window" >m/z window</option>
		</param>
		<when value="list">
			<param name="mzList" type="text" area="true" size="7x70" label="m/z list" 
				help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here.">
				<sanitizer>
					<!-- this translates from line-separated to comma separated list, removes quotes -->
					<valid/>
					<mapping initial="none">
				    	<add source="&#10;" target=","/>
				    	<add source="&#13;" target=""/>
				    	<add source="&quot;" target=""/>
		 			</mapping>
				</sanitizer>
			</param>
			<param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)"  />
		</when>
		<when value="window">
			<param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" />
			<param name="mzEnd" type="float" value="" size="10"  label="m/z end" help="End of m/z window" />
   		</when>
	</conditional>		 
	

	<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. Here 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, removes quotes  -->
			<valid/>
			<mapping initial="none">
		    	<add source="&#10;" target=","/>
		    	<add source="&#13;" target=""/>
		    	<add source="&quot;" target=""/>
 			</mapping>
		</sanitizer>	
	</param>
	
	<param name="combineSamples" type="select" size="50" label="Combine samples in EIC" 
	       help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot 
	       only contains the EIC of the m/z in the respectively given sample (the sample name from the sample list in the same position as the
	       m/z in the m/z list.). Tip: use Yes for visualizing EIC of grouped masses (MsClust or CAMERA groups), use No for visualizing EICs of the same mass in 
	       the different samples.">
		<option value="No" selected="true">No</option>
		<option value="Yes" >Yes</option>
	</param>
	<param name="rtPlotMode" type="select" size="50" label="RT plot mode" 
	       help="Select whether EIC should be on original or raw Retention Time">
		<option value="raw" selected="true">Raw</option>
		<option value="corrected" >Corrected</option>
	</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 will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method. 
It produces a HTML report showing the EIC plots, one for each given mass. The figure below shows an example of such an EIC plot.
 
.. image:: $PATH_TO_IMAGES/massEIC.png 


  </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>