view xcms_plot_chromatogram.xml @ 0:fe1f0f16d9e6 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty

<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 xcms experience</description>

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

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

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

        image '$image'

        @COMMAND_FILE_LOAD@
    ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />

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

    <outputs>
        <data name="ticsPdf" format="pdf"  label="${image.name[:-6]}.TICs.pdf" from_work_dir="TICs.pdf"/>
        <data name="bpisPdf" format="pdf" label="${image.name[:-6]}.BPIs.pdf" from_work_dir="BPIs.pdf" />
    </outputs>

    <tests>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.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
========================= ================= =================== ==========
xcms.xcmsSet              xset.RData        rdata.xcms.raw      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 the one created by xcmsSet and retcor tools.

    ]]></help>

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