comparison metams_lcms_pick_and_group.xml @ 52:5b1adc49700d

small adjustment

51:684d2341968c

		metaMS_cmd_pick_and_group.r 
	    $data_files
	    $customMetaMSsettings
	    $outputFile 
	    $xsetOut
	    $findAdducts_polarity
	    $htmlReportFile
	    $htmlReportFile.files_path
	    $outputLog
	</command>
<inputs>
	<param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDF, mzML or mzXML files)" help=".zip file containing the CDF, mzML or mzXML files of the new measurements"/>
	
	<param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP" 
		help="Choose a name to give for the specific settings in the parameters below"/><!-- TODO - let user choose this -->
	
	
	<!-- ===========NB : if peak picking, alignment OR CAMERA settings have to be reused for runGC wrapper in the future, we can use Galaxy macro expansions here
	                     to avoid defining these parameters again in the runGC wrapper ========================= -->
	<conditional name="peakPicking">

			help="max. number of expected isotopes" />	
			
	<param name="findIsotopes_minfrac" type="float" size="10" value="0.5" label="(findIsotopes)minfrac" 
		help="The ratio for the number of samples, which must satisfy the C12/C13 rule for isotope annotation" />					
	
	<param name="findAdducts_polarity" type="select" size="30" label="(findAdducts)polarity" 
		help="Which polarity mode was used for measuring of the ms sample">
		<option value="positive" selected="true">positive</option>
		<option value="negative" >negative</option>
	</param>

	<param name="findAdducts_multiplier" type="integer" size="10" value="3" label="(findAdducts)multiplier" 
			help="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" />

52:5b1adc49700d

		metaMS_cmd_pick_and_group.r 
	    $data_files
	    $customMetaMSsettings
	    $outputFile 
	    $xsetOut
	    $polarity
	    $htmlReportFile
	    $htmlReportFile.files_path
	    $outputLog
	</command>
<inputs>
	<param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDF, mzML or mzXML files)" help=".zip file containing the CDF, mzML or mzXML files of the new measurements"/>
	
	<param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP" 
		help="Choose a name to give for the specific settings in the parameters below"/><!-- TODO - let user choose this -->
	
	<param name="polarity" type="select" size="30" label="polarity" 
		help="Which polarity mode was used for measuring of the ms sample">
		<option value="positive" selected="true">positive</option>
		<option value="negative" >negative</option>
	</param>
	
	
	<!-- ===========NB : if peak picking, alignment OR CAMERA settings have to be reused for runGC wrapper in the future, we can use Galaxy macro expansions here
	                     to avoid defining these parameters again in the runGC wrapper ========================= -->
	<conditional name="peakPicking">

			help="max. number of expected isotopes" />	
			
	<param name="findIsotopes_minfrac" type="float" size="10" value="0.5" label="(findIsotopes)minfrac" 
		help="The ratio for the number of samples, which must satisfy the C12/C13 rule for isotope annotation" />					
	

	<param name="findAdducts_multiplier" type="integer" size="10" value="3" label="(findAdducts)multiplier" 
			help="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" />