comparison abims_xcms_group.xml @ 3:98e33cdf0eb1 draft

planemo upload

2:ed149026836e

<tool id="abims_xcms_group" name="xcms.group" version="2.0.2">

    <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>

    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="2.1">xcms_w4m_script</requirement>
    </requirements>

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

    <command>
        xcms.r 
        xfunction group image $image method $methods.method sleep 0.001 
        #if $methods.method == "density":
            ## minsamp $methods.minsamp 
            minfrac $methods.minfrac 
            bw $methods.bw 
            mzwid $methods.mzwid

            mzVsRTbalance $methods.mzVsRTbalance
            mzCheck $methods.mzCheck
            rtCheck $methods.rtCheck
            kNN $methods.kNN
        #end if
        && (
        mv group.RData $xsetRData;
        mv Rplots.pdf $rplotsPdf
        );
        cat xset.log
   </command> 

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
        <conditional name="methods">
            <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
        <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
    </outputs>

    <tests>
        <test>
            <param name="image" value="xset.RData"/>

            <param name="methods.bw" value="5"/>
            <param name="methods.minfrac" value="0.3"/>
            <param name="methods.mzwid" value="0.01"/>
            <param name="methods.density_options.option" value="show"/>
            <param name="methods.density_options.max" value="50"/>
            <output name="xsetRData" file="xset.group.RData" />
            <output name="rplotsPdf" file="xset.group.Rplots.pdf" />
         
        </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] 

.. image:: xcms_group.png
        :width: 700



    </help>


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

3:98e33cdf0eb1

<tool id="abims_xcms_group" name="xcms.group" version="2.0.4">

    <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>

    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
    </requirements>

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

    <command><![CDATA[
        xcms.r 
        xfunction group 
        image $image 

        xsetRdataOutput $xsetRData
        rplotspdf $rplotsPdf

        method $methods.method sleep 0.001 
        #if $methods.method == "density":
            ## minsamp $methods.minsamp 
            minfrac $methods.minfrac 
            bw $methods.bw 
            mzwid $methods.mzwid

            mzVsRTbalance $methods.mzVsRTbalance
            mzCheck $methods.mzCheck
            rtCheck $methods.rtCheck
            kNN $methods.kNN
        #end if
        ;
        return=\$?;
        mv log.txt $log;
        cat $log;
        sh -c "exit \$return"
        
   ]]></command> 

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
        <conditional name="methods">
            <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
        <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
    </outputs>

    <tests>
        <test>
            <param name="image" value="xset.RData"/>

            <param name="methods.bw" value="5"/>
            <param name="methods.minfrac" value="0.3"/>
            <param name="methods.mzwid" value="0.01"/>
            <param name="methods.density_options.option" value="show"/>
            <param name="methods.density_options.max" value="50"/>
            <!--<output name="xsetRData" file="xset.group.RData" />-->
            <!--<output name="rplotsPdf" file="xset.group.Rplots.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: 6642" />
                    <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] 

.. image:: xcms_group.png
        :width: 700


---------------------------------------------------

Changelog/News
--------------

**Version 2.0.4 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs

- UPDATE: refactoring to feed the new report tool


**Version 2.0.2 - 02/06/2015**

- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.


    ]]></help>


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