comparison metams_lcms_annotate.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.

48:26b93438f30e

<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.3">
	<description> Runs metaMS process for LC/MS feature grouping and annotation</description>
	<requirements>
		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
	</requirements>	
	<command interpreter="Rscript">
		metaMS_cmd_interface.r 
	    $constructed_db
	    $data_files
	    $customMetaMSsettings
	    $outputFile 
	    $outputLog
	    $xsetOut
	    $htmlReportFile
	    $htmlReportFile.files_path
	</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="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDFs)" help=".zip file containing the CDF files of the new measurements"/>
	
	
	
	<param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
	
	<param name="method" type="select" size="30" label="PEAK PICKING method =====================================================">
		<option value="matchedFilter" selected="true">matchedFilter</option>
	</param>
	<param name="step" type="float" size="10" value="0.05" label="step" help="step"/>
	<param name="fwhm" type="integer" size="10" value="20" label="fwhm" help="fwhm" />
	<param name="snthresh" type="integer" size="10" value="4" label="snthresh" help="snthresh" />
	<param name="max" type="integer" size="10" value="50" label="max" help="max" />
	
	<param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" help="min.class.fraction"/>
	<param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" help="min.class.size" />
	<param name="mzwid" type="float" size="10" value="0.1" label="mzwid" help="mzwid"/>
	<param name="bws" type="text" size="10" value="30,10" label="bws" help="bws"/>
	<param name="missingratio" type="float" size="10" value="0.2" label="missingratio" help="missingratio"/>
	<param name="extraratio" type="float" size="10" value="0.1" label="extraratio" help="extraratio"/>
	<param name="retcormethod" type="select" size="30" label="retcormethod" help="retcormethod">
		<option value="linear" selected="true">linear</option>
	</param>
	<param name="retcorfamily" type="select" size="30" label="retcorfamily" help="retcorfamily">
		<option value="symmetric" selected="true">symmetric</option>
	</param>
	<param name="fillPeaks" type="select" size="30" label="fillPeaks" help="fillPeaks">
		<option value="TRUE" selected="true">Yes</option>
		<option value="FALSE">No</option>
	</param>
	<param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" help="perfwhm"/>
	<param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" help="cor_eic_th" />
	<param name="ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
	<param name="rtdiff" type="float" size="10" value="1.5" label="MATCH2DB 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" />
	

<configfiles>

<configfile name="customMetaMSsettings">## start comment
		## metaMS process settings
		customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
                            chrom = "LC",
                            PeakPicking = list(
                              method = "${method}",
                              step = ${step},
                              fwhm = ${fwhm},
                              snthresh = ${snthresh},
                              max = ${max}),
                            Alignment = list(
                              min.class.fraction = ${min_class_fraction},
                              min.class.size = ${min_class_size},
                              mzwid = ${mzwid},
                              bws = c(${bws}),
                              missingratio = ${missingratio},
                              extraratio = ${extraratio},
                              retcormethod = "${retcormethod}",
                              retcorfamily = "${retcorfamily}",            
                              fillPeaks = ${fillPeaks}),
                            CAMERA = list(
                              perfwhm = ${perfwhm},
                              cor_eic_th = ${cor_eic_th},
                              ppm= ${ppm}))
metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
            rtdiff = ${rtdiff},
            rtval = ${rtval},
            mzdiff = ${mzdiff},
            ppm = ${match2DB_ppm},

</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 ${on_string} - metaMS LOG"/>
	<data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - metaMS xcmsSet (RDATA)"/>
	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
</outputs>
<tests>
	<test>
	</test>

<code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
<help>

.. class:: infomark
  
Runs metaMS process for LC/MS feature grouping and annotation. Parts of the metaMS process also make use of the XCMS and CAMERA tools and algorithms.
The figure below shows the main parts of the metaMS process. 

.. image:: $PATH_TO_IMAGES/metaMS.png 


**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

49:f772a5caa86a

<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" />
	

<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},

</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>

<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: