<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(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-class.xset.merged.group.retcor.RData" ftype="rdata"/>
            <expand macro="test_file_load_single"/>
            <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
            <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
            <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
        </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 Current chromatogram (TIC) from xcms experiments.


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

**Upstream tools**

=========================== ======================== ==============================
Name                        Output file              Format
=========================== ======================== ==============================
MSnbase.readMSData          ``*``.raw.RData          rdata.msnbase.raw
--------------------------- ------------------------ ------------------------------
xcms.findChromPeaks         ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
--------------------------- ------------------------ ------------------------------
xcms.findChromPeaks Merger  xset.merged.RData        rdata.xcms.retcor
--------------------------- ------------------------ ------------------------------
xcms.adjustRtime            ``*``.adjustRtime.RData  rdata.xcms.retcor
=========================== ======================== ==============================

.. 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)

@HELP_XCMS_MANUAL@

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

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

@HELP_XCMS_NEWVERSION_31200@

**Galaxy Version 3.6.1+galaxy2 - 23/09/2020**

- BUGFIX: sample group colours did not match group labels.

@HELP_XCMS_NEWVERSION_3610@

@HELP_XCMS_NEWVERSION_3440@

**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>