annotate abims_xcms_summary.xml @ 12:27e7da5f6848 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797

<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3">

    <description>Create a summary of XCMS analysis</description>

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

    <requirements>
        <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
        <requirement type="package" version="1.1_4">r-batch</requirement>
    </requirements>

    <expand macro="stdio"/>

    <command><![CDATA[
        $__tool_directory__/xcms_summary.r

        image '$image'
        htmlOutput '$htmlOutput'
        user_email $__user_email__

    ]]></command>

    <inputs>

        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />

    </inputs>

    <outputs>
        <data name="htmlOutput" format="html" label="xcms summary html" />
    </outputs>

    <tests>
        <test>
            <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
            <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" />
            <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

============
Xcms.summary
============

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

This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools

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

**Upstream tools**

========================= ================= ===================== ==========
Name                      output file       format                parameter
========================= ================= ===================== ==========
xcms.xcmsSet              xset.RData        rdata.xcms.raw        RData file
------------------------- ----------------- --------------------- ----------
xcms.group                xset.RData        rdata.xcms.group      RData file
------------------------- ----------------- --------------------- ----------
xcms.retcor               xset.RData        rdata.xcms.retcor     RData file
------------------------- ----------------- --------------------- ----------
xcms.fillpeaks            xset.RData        rdata.xcms.fillpeaks  RData file
------------------------- ----------------- --------------------- ----------
CAMERA.annotate           xset.RData        rdata.camera.*        RData file
========================= ================= ===================== ==========


.. image:: xcms_summary_workflow.png

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

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

**Version 1.0.3 - 03/02/2017**

- IMPROVEMENT: xcms.summary can deal with merged individual data

**Version 1.0.2 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 1.0.1 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**Version 1.0.0 - 10/02/2016**

- NEW: Create a summary of XCMS analysis


    ]]></help>


    <expand macro="citation" />

</tool>