comparison abims_CAMERA_annotateDiffreport.xml @ 1:a887bff50e45 draft

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0:b495191430d5

<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1">

    <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>

    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command>
        CAMERA.r 
        xfunction annotatediff image $image
        convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1}
        sigma $sigma perfwhm $perfwhm 
        maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
        ppm $ppm mzabs $mzabs intval $intval 
        max_peaks $max_peaks
        quick $quick_block.quick

            value $options.value
            sortpval $options.sortpval 
            h $options.h
            w $options.w
            mzdec $options.mzdec
        #else
            eicmax 0
            eicwidth 200
            value "into"
            sortpval TRUE 
            h 480
            w 640
            mzdec 2
        #end if
        && (
            mv variableMetadata.tsv $variableMetadata;
            mv dataMatrix.tsv $datamatrix;
            mv annotatediff.RData $rdata
        );
        cat xset.log
        
      
    </command>

    <inputs>
    
    
        <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />

        <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
        <param name="num_digits" type="integer" value="0" label="" help="Number of decimal places for mass values reported in ions identifiers" />

        <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" />
        <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" />
        <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" />
        <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" />

        </conditional>
       
    </inputs>

    <outputs>
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" >
            <discover_datasets pattern="__designation_and_ext__" directory="zip" visible="true" />
        </data>
        <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
        <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" >
            <change_format>
                <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
                <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
            </change_format>
        </data>    
    </outputs>
    
    <tests>
        <test>
            <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>

        </test>
    </tests>
    
    
    
    <help>
        
.. class:: infomark

**Authors** Carsten Kuhl [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann sneumann@@ipb-halle.de

**Example of a part of xset.annotate.variableMetadata.tsv output** 

.. image:: annotatediffreport_variableMetadata.png

    </help>

    <citations>
        <citation type="doi">10.1021/ac202450g</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

1:a887bff50e45

<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.2">

    <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>

    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command><![CDATA[
        CAMERA.r 
        xfunction annotatediff 
        image $image

        variableMetadataOutput $variableMetadata
        dataMatrixOutput $datamatrix
        xsetRdataOutput $rdata

        convert_param $convert_param num_digits $num_digits 
        nSlaves \${GALAXY_SLOTS:-1}
        sigma $sigma perfwhm $perfwhm 
        maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
        ppm $ppm mzabs $mzabs intval $intval 
        max_peaks $max_peaks
        quick $quick_block.quick

            value $options.value
            sortpval $options.sortpval 
            h $options.h
            w $options.w
            mzdec $options.mzdec
            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
        #else
            eicmax 0
            eicwidth 200
            value "into"
            sortpval TRUE 
            h 480
            w 640
            mzdec 2
            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
        #end if
        
      
    ]]></command>

    <inputs>
    
    
        <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />

        <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
        <param name="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" />

        <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" />
        <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" />
        <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" />
        <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" />

        </conditional>
       
    </inputs>

    <outputs>
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
        <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
        <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" >
            <change_format>
                <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
                <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
            </change_format>
        </data>
	<data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
		 <filter>(options['option'] == 'show')</filter>
	</data>    
    </outputs>
    
    <tests>
        <test>
            <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>

        </test>
    </tests>
    
    
    
    <help><![CDATA[
        
.. class:: infomark

**Authors** Carsten Kuhl [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann sneumann@@ipb-halle.de

**Example of a part of xset.annotate.variableMetadata.tsv output** 

.. image:: annotatediffreport_variableMetadata.png

    ]]></help>

    <citations>
        <citation type="doi">10.1021/ac202450g</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>