comparison abims_xcms_retcor.xml @ 7:bb602a5b8819 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093

6:123824c7eaa8

<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.7">

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

    <macros>
        <import>macros.xml</import>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@ 
        image $image 
        xfunction retcor 

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

            #end if
        #end if

        @COMMAND_ZIPFILE_LOAD@

        @COMMAND_LOG_EXIT@        
    ]]></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">

                <option value="obiwarp" >obiwarp</option>
                <option value="peakgroups" selected="peakgroups">peakgroups</option>
            </param>
            <when value="obiwarp">
                <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
            </when> 
            <when value="peakgroups">   
                <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
                    <option value="loess">loess</option>
                    <option value="linear">linear</option>
                </param>
                <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />

                        <option value="show">show</option>
                        <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>

        </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|method" value="peakgroups"/>
            <param name="methods|smooth" value="loess"/>

            </output>
        </test>
    </tests>

    <help><![CDATA[
        
@HELP_AUTHORS@

===========
Xcms.retcor
===========

-----------
Description
-----------

After matching peaks into groups, xcms can use those groups to identify and correct 
correlated drifts in retention time from run to run. The aligned peaks can then be 
used for a second pass of peak grouping which will be more accurate than the first. 
The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful 
for identifying retention time drifts. Some groups may be missing peaks from a large 
fraction of samples and thus provide an incomplete picture of the drift at that time point. 
Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.

.. class:: warningmark

**After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is

    | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step

xset.group.retcor.RData: rdata.xcms.retcor format

    | Rdata file that will be necessary in the **xcms.group** step of the workflow.
    
    
------

.. class:: infomark 

The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.

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

---------------
Working example
---------------

    | missing -> **1**
    | Advanced options: -> **show**
    | span -> **0.2**
    | family -> **gaussian**
    | plottype -> **deviation**
    

Output files
------------

    | **1) xset.group.retcor.RData: RData file**

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

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

**Version 2.0.7 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 2.0.6 - 04/04/2016**

7:bb602a5b8819

<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.8">

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

    <macros>
        <import>macros.xml</import>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        image $image
        xfunction retcor

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

            #end if
        #end if

        @COMMAND_ZIPFILE_LOAD@

        @COMMAND_LOG_EXIT@
    ]]></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">

                <option value="obiwarp" >obiwarp</option>
                <option value="peakgroups" selected="peakgroups">peakgroups</option>
            </param>
            <when value="obiwarp">
                <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
            </when>
            <when value="peakgroups">
                <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
                    <option value="loess">loess</option>
                    <option value="linear">linear</option>
                </param>
                <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />

                        <option value="show">show</option>
                        <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>

        </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|method" value="peakgroups"/>
            <param name="methods|smooth" value="loess"/>

            </output>
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

===========
Xcms.retcor
===========

-----------
Description
-----------

After matching peaks into groups, xcms can use those groups to identify and correct
correlated drifts in retention time from run to run. The aligned peaks can then be
used for a second pass of peak grouping which will be more accurate than the first.
The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
for identifying retention time drifts. Some groups may be missing peaks from a large
fraction of samples and thus provide an incomplete picture of the drift at that time point.
Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.

.. class:: warningmark

**After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is

    | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step

xset.group.retcor.RData: rdata.xcms.retcor format

    | Rdata file that will be necessary in the **xcms.group** step of the workflow.


------

.. class:: infomark

The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.


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

---------------
Working example
---------------

    | missing -> **1**
    | Advanced options: -> **show**
    | span -> **0.2**
    | family -> **gaussian**
    | plottype -> **deviation**


Output files
------------

    | **1) xset.group.retcor.RData: RData file**

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

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

**Version 2.0.8 - 22/12/2016**

- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph

**Version 2.0.7 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 2.0.6 - 04/04/2016**