annotate abims_xcms_group.xml @ 10:c81275aee959 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797

<tool id="abims_xcms_group" name="xcms.group" version="2.1.0">

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

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

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

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        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
        #if $methods.density_options.option == "show":
            max $methods.density_options.max
        #end if
        #elif $methods.method == "mzClust":
            mzppm $methods.mzppm
            mzabs $methods.mzabs
            minfrac $methods.minfrac
            ## minsamp $methods.minsamp
        #else:
            mzVsRTbalance $methods.mzVsRTbalance
            mzCheck $methods.mzCheck
            rtCheck $methods.rtCheck
            kNN $methods.kNN
        #end if

        @COMMAND_PEAKLIST@

        @COMMAND_LOG_EXIT@
   ]]></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">
                <option value="density" selected="true">density</option>
                <option value="mzClust" >mzClust</option>
                <option value="nearest" >nearest</option>
            </param>
            <when value="density">
                <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
                <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
                <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
<!--
                <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
-->
            <conditional name="density_options">
            <param name="option" type="select" label="Advanced options">
                <option value="show">show</option>
                <option value="hide" selected="true">hide</option>
            </param>
            <when value="show">
                <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
            </when>
            <when value="hide">
            </when>
        </conditional>

            </when>
            <when value="mzClust">
                <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
                <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
                <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />
<!--
                <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
-->
            </when>
            <when value="nearest">
                <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" />
                <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
                <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
                <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
            </when>
        </conditional>
<!--
        <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines">
            <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
        </param>
-->

        <expand macro="input_peaklist"/>
    </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"/>
        <expand macro="output_peaklist" function="group"/>
        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
    </outputs>

    <tests>
        <!--<test>
            <param name="image" value="xset.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 48998" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="image" value="faahKO.xset.RData"/>
            <param name="methods|method" value="density"/>
            <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"/>
            <conditional name="peaklist">
                <param name="convertRTMinute" value="false" />
                <param name="peaklistBool" value="true" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 8275" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
            <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
            <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
        </test>
        <test>
            <param name="image" value="faahKO-single-class.xset.merged.RData"/>
            <param name="methods|method" value="density"/>
            <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"/>
            <conditional name="peaklist">
                <param name="convertRTMinute" value="false" />
                <param name="peaklistBool" value="true" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 8275" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
            <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
            <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 664" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="image" value="MM-single.xset.merged.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 2 samples" />
                    <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
                    <has_text text="Mass range: 117.0357-936.7059 m/z" />
                    <has_text text="Peaks: 236 (about 118 per sample)" />
                    <has_text text="Peak Groups: 236" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <!--<test>
            <param name="image" value="xset.group.retcor.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 48958" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="image" value="faahKO.xset.group.retcor.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 8157" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
            <param name="methods|method" value="density"/>
            <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="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 8157" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

==========
Xcms.Group
==========

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

After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.



-----------------
Workflow position
-----------------

**Upstream tools**

========================= ================= =================== ==========
Name                      output file       format              parameter
========================= ================= =================== ==========
xcms.xcmsSet              xset.RData        rdata.xcms.raw      RData file
------------------------- ----------------- ------------------- ----------
xcms.xcmsSet Merger       xset.RData        rdata.xcms.raw      RData file
------------------------- ----------------- ------------------- ----------
xcms.retcor               xset.RData        rdata.xcms.retcor   RData file
========================= ================= =================== ==========


**Downstream tools**

+---------------------------+--------------------------------------+
| Name                      | Output file     | Format             |
+===========================+=================+====================+
|xcms.retcor                | xset.RData      | rdata.xcms.group   |
+---------------------------+--------------------------------------+
|xcms.fillPeaks             | xset.RData      | rdata.xcms.group   |
+---------------------------+--------------------------------------+

The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.

**General schema of the metabolomic workflow**

.. image:: xcms_group_workflow.png


-----------
Input files
-----------

+---------------------------+-----------------------+
| Parameter : num + label   |   Format              |
+===========================+=======================+
| Or : RData file            |   rdata.xcms.raw     |
+---------------------------+-----------------------+
| Or : RData file            |   rdata.xcms.retcor  |
+---------------------------+-----------------------+


----------
Parameters
----------

Method to use for grouping
--------------------------

**mzClust**

    | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**.

**density**

    | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.

**nearest**

    | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.


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

xset.group.Rplots.pdf

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

    | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).


------

.. class:: infomark

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


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


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

Input files
-----------

    | RData file -> **xset.RData**

Parameters
----------

    | Method -> **density**
    | bw     -> **5**
    | minfrac -> **0.3**
    | mzwid    -> **0.01**
    | Advanced options: **show**
    | max -> **50**


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

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

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

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


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

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

**Version 2.1.0 - 07/02/2017**

- IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate

- IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"

- BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50

**Version 2.0.6 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 2.0.5 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**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>


    <expand macro="citation" />


</tool>