annotate xcms_differential_analysis.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.

<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis"  version="0.0.4">
	<description> Runs xcms diffreport function for differential Analsysis</description>
	<requirements>
		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
	</requirements>	
	<command interpreter="Rscript">
		xcms_differential_analysis.r 
	    $xsetData
		"$class1"
		"$class2"
		$topcount
		$outTable 
		$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="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/>
	<param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/>
	
	<param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
	
</inputs>
<outputs>
	<data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
</outputs>
<tests>
	<test>
	</test>
</tests>
<help>

.. class:: infomark
  
Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for 
the most significant differences. The figure below shows an example of such an EIC.

.. image:: $PATH_TO_IMAGES/diffreport.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>