comparison abims_xcms_xcmsSet.xml @ 1:2f5b78be1dd6 draft

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0:1bad16e5e4ae

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>

    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <command>
        xcms.r
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":
            zipfile $inputs.zip_file
        #end if

        xfunction xcmsSet
        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
        #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
            #end if 
            #if $methods.options_c.option == "show":
                mzdiff $methods.options_c.mzdiff
                snthresh $methods.options_c.snthresh
                integrate $methods.options_c.integrate
                noise $methods.options_c.noise
                prefilter "c($methods.options_c.prefilter)"
            #end if
        #elif $methods.method == "matchedFilter":
            step $methods.step
            fwhm $methods.fwhm
            #if $methods.options_m.option == "show":
                ## sigma "$methods.options_m.sigma"

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        && (mv xcmsSet.RData $xsetRData;
        mv sampleMetadata.tsv $sampleMetadata;
        mv TICs_raw.pdf $ticsRawPdf;
        mv BPCs_raw.pdf $bpcsRawPdf;
        mv xset.log $log);
        cat $log
    </command>
    
    <inputs>

        <conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >

                    <when value="show">
                        <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
                            <validator type="empty_field"/> 
                        </param>
                    </when>
                </conditional>
                        
                <conditional name="options_c">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>

                            <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
                            <option value="2">peak limits based on real data (more sensitive to noise)</option>
                        </param>
                        <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                        <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                    </when>
                </conditional>
            </when>

        <!-- matched Filter options -->

                        <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
<!--
                        <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
-->
                    </when>
                </conditional>
            </when>

        <!-- MSW Filter options -->
            <when value="MSW">

            <param name="methods.fwhm" value="4" />
            <param name="methods.options_m.option" value="show" />
            <param name="methods.options_m.max" value="50" />
            <param name="methods.options_m.snthresh" value="1" />
            <param name="methods.options_m.steps" value="2" />
            <output name="xsetRData" file="xset.RData" />
            <output name="sampleMetadata" file="sampleMetadata.tsv" />
            <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
            <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
            <output name="log" file="xset.log.txt" />
        </test>
    </tests>
    
    <help>

.. class:: infomark

**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail] 

    | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**

.. image:: xcms_tics.png


    </help>


    <citations>
        <citation type="doi">10.1021/ac051437y</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>

1:2f5b78be1dd6

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.5">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>

    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <command><![CDATA[
        xcms.r
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":
            zipfile $inputs.zip_file
        #end if

        xfunction xcmsSet

        xsetRdataOutput $xsetRData
        sampleMetadataOutput $sampleMetadata
        ticspdf $ticsRawPdf
        bicspdf $bpcsRawPdf

        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
        #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
        #end if 
        #if $methods.options_c.option == "show":
            mzdiff $methods.options_c.mzdiff
            snthresh $methods.options_c.snthresh
            integrate $methods.options_c.integrate
            noise $methods.options_c.noise
            prefilter "c($methods.options_c.prefilter)"
        #end if
        #elif $methods.method == "matchedFilter":
            step $methods.step
            fwhm $methods.fwhm
            #if $methods.options_m.option == "show":
                ## sigma "$methods.options_m.sigma"

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        ;
        return=\$?;
        mv log.txt $log;
        cat $log;
        sh -c "exit \$return"
    ]]></command>
    
    <inputs>

        <conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >

                    <when value="show">
                        <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
                            <validator type="empty_field"/> 
                        </param>
                    </when>
                    <when value="hide">
                    </when>
                </conditional>
                        
                <conditional name="options_c">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>

                            <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
                            <option value="2">peak limits based on real data (more sensitive to noise)</option>
                        </param>
                        <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                        <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                    </when>
                    <when value="hide">
                    </when>
                </conditional>
            </when>

        <!-- matched Filter options -->

                        <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
<!--
                        <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
-->
                    </when>
                    <when value="hide">
                    </when>
                </conditional>
            </when>

        <!-- MSW Filter options -->
            <when value="MSW">

            <param name="methods.fwhm" value="4" />
            <param name="methods.options_m.option" value="show" />
            <param name="methods.options_m.max" value="50" />
            <param name="methods.options_m.snthresh" value="1" />
            <param name="methods.options_m.steps" value="2" />
            <!--<output name="xsetRData" file="xset.RData" />-->
            <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
            <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
            <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />-->
            <output name="log">
                <assert_contents>
                    <has_text text="object with 9 samples" />
                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[

.. class:: infomark

**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail] 

    | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**

.. image:: xcms_tics.png


    ]]></help>


    <citations>
        <citation type="doi">10.1021/ac051437y</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>