comparison abims_xcms_retcor.xml @ 1:da716e2937f2 draft

planemo upload

0:19c1d2598eb5

<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.2">

    <description>Retention Time Correction using retcor function from xcms R package </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 
        image $image xfunction retcor method $methods.method
        #if $methods.method == "obiwarp":
            profStep $methods.profStep
        #else
            smooth $methods.smooth
            extra $methods.extra

                span $methods.options.span
                family $methods.options.family
                plottype $methods.options.plottype
            #end if
        #end if
        && ( mv retcor.RData $xsetRData;
        mv TICs_corrected.pdf $ticsCorPdf ;
        mv BPCs_corrected.pdf $bpcsCorPdf ;
        mv Rplots.pdf $rplotsPdf 2> /dev/null);
        cat xset.log; 
        
    </command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,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 retention time correction" help="[method] See the help section below" >

                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
                        
            <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
                        <option value="gaussian" selected="true">gaussian</option>
                        <option value="symmetric">symmetric</option>
                    </param>

            <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
                            <option value="none" selected="true">none</option>
                            <option value="deviation">deviation</option>
                            <option value="mdevden">mdevden</option>
                        </param>
                    </when>
            <when value="hide">
            </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

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

            <filter>(family == 'symmetric')</filter>
            <filter>(plottype != 'none')</filter>
        </data>
        <data name="ticsCorPdf"   format="pdf"  label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
        <data name="bpcsCorPdf"   format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
    </outputs>
    
    <tests>
        <test>
            <param name="image" value="xset.group.RData"/>

            <param name="methods.missing" value="1"/>
            <param name="methods.options.option" value="show"/>
            <param name="methods.options.span" value="0.2"/>
            <param name="methods.options.family" value="gaussian"/>
            <param name="methods.options.plottype" value="deviation"/>
            <output name="xsetRData" file="xset.group.retcor.RData" />
            <output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />
            <output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />
            <output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.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] 

    | **2) Example of an xset.group.retcor.TICs_corrected pdf file**

.. image:: xcms_retcor.png

    </help>

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

1:da716e2937f2

<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.5">

    <description>Retention Time Correction using retcor function from xcms R package </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 
        image $image 
        xfunction retcor 

        xsetRdataOutput $xsetRData
        ticspdf $ticsCorPdf
        bicspdf $bpcsCorPdf
        rplotspdf $rplotsPdf

        method $methods.method
        #if $methods.method == "obiwarp":
            profStep $methods.profStep
        #else
            smooth $methods.smooth
            extra $methods.extra

                span $methods.options.span
                family $methods.options.family
                plottype $methods.options.plottype
            #end if
        #end if
        ###if $zip_file:
        ##    zipfile $zip_file
        ###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" 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 retention time correction" help="[method] See the help section below" >

                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
                        
                        <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
                            <option value="gaussian" selected="true">gaussian</option>
                            <option value="symmetric">symmetric</option>
                        </param>

                        <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
                            <option value="none" selected="true">none</option>
                            <option value="deviation">deviation</option>
                            <option value="mdevden">mdevden</option>
                        </param>
                    </when>
                    <when value="hide">
                    </when>
                </conditional>
            </when>
        </conditional>
        <!-- To pass planemo test -->
        <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />-->
    </inputs>

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

            <filter>(family == 'symmetric')</filter>
            <filter>(plottype != 'none')</filter>
        </data>
        <data name="ticsCorPdf"   format="pdf"  label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
        <data name="bpcsCorPdf"   format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
    </outputs>
    
    <tests>
        <test>
            <param name="image" value="xset.group.RData"/>

            <param name="methods.missing" value="1"/>
            <param name="methods.options.option" value="show"/>
            <param name="methods.options.span" value="0.2"/>
            <param name="methods.options.family" value="gaussian"/>
            <param name="methods.options.plottype" value="deviation"/>
            <param name="zip_file" value="sacuri.zip"/>
            <!--<output name="xsetRData" file="xset.group.retcor.RData" />-->
            <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />-->
            <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />-->
            <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />-->
            <output name="log">
                <assert_contents>
                    <has_text text="object with 9 samples" />
                    <has_text text="Time range: 0.7-1139.9 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] 

    | **2) Example of an xset.group.retcor.TICs_corrected pdf file**

.. image:: xcms_retcor.png


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

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

**Version 2.0.5 - 10/02/2016**

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

- BUGFIX: some pdf remained empty even when the process succeed

- 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>
    </citations>