comparison abims_xcms_fillPeaks.xml @ 29:f6d3e6be4ea3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

28:9b0bf28bcbaf

==============
Xcms.fillPeaks
==============

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

**Integrate areas of missing peaks**
For each sample, identify peak groups where that sample is not

"MSW" is used for peaklists without retention-time information
like those from direct-infusion spectra.



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


**Upstream tools**

========================= ================= ================== ==========
Name                      output file       format             parameter
========================= ================= ================== ==========
xcms.group                xset.group.RData  rdata.xcms.group   RData file
========================= ================= ================== ==========


**Downstream tools**

+---------------------------+------------------+-----------------------+

|CAMERA.annotate            | xset.retcor.RData| rdata.xcms.fillpeaks  |
+---------------------------+------------------+-----------------------+
|xcms.summary               | xset.retcor.RData| rdata.xcms.fillpeaks  |
+---------------------------+------------------+-----------------------+

The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.


**General schema of the metabolomic workflow**

.. image:: xcms_fillpeaks_workflow.png



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

**MSW**

    | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.


Get a Peak List
---------------

If 'true', the module generates two additional files corresponding to the peak list:
- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
- the data matrix (corresponding to related intensities)

**decimal places for [mass or retention time] values in identifiers**

    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
    | Theses parameters do not affect decimal places in columns other than the identifier one.

**Reported intensity values**

    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
    | - into: integrated area of original (raw) peak
    | - maxo: maximum intensity of original (raw) peak
    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)

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

xset.fillPeaks.RData : rdata.xcms.fillpeaks format

    | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.

xset.variableMetadata.tsv : tabular format

    | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.

xset.dataMatrix.tsv : tabular format

    | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.

------

.. class:: infomark

The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.


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

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

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

Parameters
----------

    | method -> **chrom**
    | Get a Peak List -> **false**


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

    | **xset.fillPeaks.RData: RData file**


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

Changelog/News

29:f6d3e6be4ea3

==============
Xcms.fillPeaks
==============

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

**Integrate areas of missing peaks**
For each sample, identify peak groups where that sample is not

"MSW" is used for peaklists without retention-time information
like those from direct-infusion spectra.



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


**Upstream tools**

+------------------------+------------------+--------------------+------------+
| Name                   | output file      | format             | parameter  |
+========================+==================+====================+============+
| xcms.group             | xset.group.RData | rdata.xcms.group   | RData file |
+------------------------+------------------+--------------------+------------+


**Downstream tools**

+---------------------------+------------------+-----------------------+

|CAMERA.annotate            | xset.retcor.RData| rdata.xcms.fillpeaks  |
+---------------------------+------------------+-----------------------+
|xcms.summary               | xset.retcor.RData| rdata.xcms.fillpeaks  |
+---------------------------+------------------+-----------------------+

**General schema of the metabolomic workflow**

.. image:: xcms_fillpeaks_workflow.png

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

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

**MSW**

    | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.

@HELP_GET_PEAK_LIST@

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

xset.fillPeaks.RData : rdata.xcms.fillpeaks format

    | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.

@HELP_GET_PEAK_LIST_OUTPUTS@


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

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

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

Parameters
----------

    | **method**: chrom


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

Changelog/News