annotate metaMS_plot.xml @ 0:b60dc620bd14 draft

planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522

 <tool id="metams_plot" name="metaMS.plot" version="1.0.0">

    <description>GC-MS data preprocessing using metaMS package</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements">
        <requirement type="package" version="9.22">ghostscript</requirement>
    </expand>
    <expand macro="stdio"/>

    <command><![CDATA[
    @COMMAND_RSCRIPT@/metaMS_plot.r
        
        metaMS '$metaMS'

        selecttic $selectedtic

        selectbpc $selectedbpc

        selecteic $selectedeic.EIC
        
        #if $selectedeic.EIC == "true"
            unkn "c($selectedeic.unkn)"
        #else
            unkn "none"
        #end if

        @COMMAND_FILE_LOAD@

    ]]></command>

    <inputs>

        <param name="metaMS" type="data" format="rdata" label="Rdata from new_metaMS_runGC" help="Rdata file containing a metaMS preprocess object" />
        <param name="selectedtic" type="boolean" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for TIC(s) ?" />
        <param name="selectedbpc" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for BPC(s) ?"  type="boolean" />

        <conditional name="selectedeic">
            <param name="EIC" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for EIC(s) ?"  type="boolean">
                <option value="false">no</option>
                <option value="true">yes</option>
            </param>
            <when value="true">
                <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12  (means 1 4 and 12). For all EIC use 0" /> 
            </when>
            <when value="false"/>
        </conditional>

        <expand macro="input_file_load"/>

    </inputs>

    <outputs>
    
        <!-- Only when user selected TIC option -->
        <data name="ticsRawPdf"   format="pdf" from_work_dir="TICs_raw.pdf" label="TICs_raw.pdf">
            <filter>selectedtic is True</filter>
        </data>
        <!-- Only when user selected BPC option -->
        <data name="bpcsRawPdf"   format="pdf" from_work_dir="BPCs_raw.pdf" label="BPCs_raw.pdf">
            <filter>selectedbpc is True</filter>
        </data>
        <!-- Only when user selected EIC option -->
        <data name="unknownPdf"   format="pdf" from_work_dir="GCMS_EIC.pdf" label="GCMS_EIC.pdf">
            <filter>selectedeic['EIC'] is True</filter>
        </data>

    </outputs>

    <tests>

        <!-- Test TIC -->
        <test>
            <param name="metaMS" value="runGC_test.RData"  ftype="rdata" />
            <expand macro="test_file_load_alg_symlink" />
            <param name="selectedtic" value="true"/>
            <output name="ticsRawPdf" value="TICs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
        </test>
        <!-- Test BPC -->
        <test>
            <param name="metaMS" value="runGC_noDB.RData"  ftype="rdata" />
            <expand macro="test_file_load_alg_symlink" />
            <param name="selectedbpc" value="true"/>
            <output name="bpcsRawPdf" value="BPCs_raw.pdf" ftype="pdf" compare="sim_size" delta="2000"/>
        </test>
        <!-- Test EICs -->
        <test>
            <param name="metaMS" value="runGC_noDB.RData"  ftype="rdata" />
            <expand macro="test_file_load_alg_symlink" />
            <conditional name="selectedeic">
                <param name="EIC" value="true"/>
                <param name="unkn" value="1:5"/>
            </conditional>
            <output name="unknownPdf" value="GCMS_EIC_noDB.pdf" ftype="pdf" compare="sim_size" delta="1200"/>
        </test>

        <!-- Tests with DB comparison -->
        <!-- Test TIC -->
        <!--<test>
            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
            <param name="selectedtic|TIC" value="true"/>
            <output name="ticsRawPdf" value="TICs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
        </test>
        --><!-- Test BPC -->
        <!--<test>
            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
            <param name="selectedbpc|BPC" value="true"/>
            <output name="bpcsRawPdf" value="BPCs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
        </test>
        --><!-- Test EICs -->
        <!--<test>
            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
            <param name="selectedeic|EIC" value="true"/>
            <output name="unknownPdf" value="GCMS_EIC.pdf" ftype="pdf" compare="sim_size" delta="600"/>
        </test>
-->
    </tests>
    
    <help>

<!--
TODO : Add test on EICs (problem with gs not found whereas I added pip install ghostscript and bgs in .travis.yml)
-->

.. class:: infomark

**Author(s)**  Ron Wehrens ([e-mail]), Georg Weingart, Fulvio Mattivi

.. class:: infomark

**Galaxy wrapper and scripts developpers** Guitton Yann LABERCA [e-mail] and Saint-Vanne Julien [e-mail]

.. class:: infomark

**Please cites**  
 
 metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B.

 xcms :   Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787.


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

====================
metaMS_plot
====================
------------
Description
------------

This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.

It will compare with opposite graphs your different classes given by a samplemetadata file or from xcms.findchrompeaks Merger tool.

It can also make EICs from your unknowns that you choose, with their pseudospectra.
  

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


**Upstream tools**

You must use result file from :

========================= ==================== ======= ==========
Name                      output file          format  parameter
========================= ==================== ======= ==========
metaMS_runGC              runGC.RData           RData   file                     
========================= ==================== ======= ==========



**General schema of the metabolomic workflow for GCMS**

.. image:: workflow_metaMS_plot.png

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

This tool always take files output from metaMS_runGC

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : RData file            |   RData    |
+---------------------------+------------+


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

There is no specific parameters except the choice for your EICs.

----------
Outputs
----------

According to your choice(s), you can have different output(s) :

- The output file **BPCs_raw.pdf** is a pdf file where each page contain BPC of a class opposed to an other class.
- The output file **TICs_raw.pdf** is a pdf file where each page contain TIC of a class opposed to an other class.
- The output file **GCMS_EIC.pdf** is a pdf file where pages contain EICs from each sample for each unknown of your choice.


----------------
Working Example
----------------
.. class:: warningmark  

**Reference Data for testing are taken from:**

Dittami,S.M. et al. (2012) *Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae): Adaptation to low salinities in Ectocarpus.* The Plant Journal

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

    | **RData file** -> runGC_test.RData

Parameters
----------

    | TIC -> **TRUE**
    | BPC -> **TRUE**
    | EIC -> **TRUE**
        | Unkn -> **1-5**


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

    | **1) TICs_raw.pdf (Total Ion Chromatogram) :**

    .. image:: BPCs_raw.pdf

    | **2) BPCs_raw.pdf (Base Peak Chromatograms) :**

    .. image:: TICs_raw.pdf

    | **3) GCMS_EIC.pdf (Extracted Ion Chromatogram) :**

    .. image:: GCMS_EIC.pdf


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

Changelog/News
--------------
**Version 1.0 - 20/05/2019**

- NEW: new tool extract from previous metaMS_runGC tool

    </help>

    <citations>
        <citation type="doi">10.1016/j.jchromb.2014.02.051</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

</tool>