view xcms_plot_chromatogram.xml @ 2:e6fdadaf039e draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
    <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from MSnbase or xcms experience(s)</description>

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

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

    <command><![CDATA[
        @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r

        images 'c("${"\",\"".join(map(str, $images))}")'

        #if str($sampleMetadata) != 'None':
            sampleMetadata '$sampleMetadata'
        #end if

        @COMMAND_FILE_LOAD@
    ]]></command>

    <inputs>
        <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
        <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>

        <expand macro="input_file_load"/>
    </inputs>

    <outputs>
        <data name="ticsPdf" format="pdf"  label="TICs.pdf" from_work_dir="TICs.pdf"/>
        <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
    </outputs>

    <tests>
        <test>
            <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
            <expand macro="test_file_load_single"/>
            <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
            <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
        </test>
        <!-- DISABLE FOR TRAVIS
        <test>
            <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
            <expand macro="test_file_load_single"/>
            <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
            <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
        </test>
        -->
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

======================
xcms plot chromatogram
======================

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

This tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience


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

**Upstream tools**

========================= ================= ============================== ==========
Name                      output file       format                         parameter
========================= ================= ============================== ==========
MSnbase readMSData        raw.RData         rdata.msnbase.raw              RData file
------------------------- ----------------- ------------------------------ ----------
xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
------------------------- ----------------- ------------------------------ ----------
xcms.retcor               xset.RData        rdata.xcms.retcor              RData file
========================= ================= ============================== ==========

.. image:: xcms_plot_chromatogram_workflow.png

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

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

**Total Ion Current (TIC) chromatogram**
    | Sum of intensity (Y) of all ions detected at each retention time(X)

**Base Peak Intensity Chromatogram (BPI)**
    | Sum of intensity (Y) of the most intense peaks at each retention time(X)

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

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

**Version 3.0.0.0 - 07/03/2018**

- NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.

    ]]></help>

    <expand macro="citation" />
</tool>