annotate abims_xcms_summary.xml @ 29:2a2850fdf29e draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e

<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

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

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

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
        <requirement type="package" version="1.46.0">bioconductor-camera</requirement>
        <requirement type="package" version="1.1_5">r-batch</requirement>
    </requirements>

    <expand macro="stdio"/>

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

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

    ]]></command>

    <inputs>

        <param name="image" type="data" format="rdata.xcms.findchrompeaks,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" ftype="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" ftype="rdata"/>
            <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" lines_diff="2"/>
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

====================
xcms process history
====================

-----------
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
========================= =========================== ================================
xcms.findChromPeaks       xset.RData                  rdata.xcms.findchrompeaks
------------------------- --------------------------- --------------------------------
xcms.groupChromPeaks      ``*``.groupChromPeaks.RData rdata.xcms.group
------------------------- --------------------------- --------------------------------
xcms.adjustRtime          ``*``.adjustRtime.RData     rdata.xcms.retcor
------------------------- --------------------------- --------------------------------
xcms.fillChromPeaks       ``*``.fillChromPeaks.RData  rdata.xcms.fillpeaks
------------------------- --------------------------- --------------------------------
CAMERA.annotate           ``*``.annotate.*.RData      rdata.camera.``*``
========================= =========================== ================================


.. image:: xcms_summary_workflow.png

@HELP_XCMS_MANUAL@

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

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

@HELP_XCMS_NEWVERSION_31200@

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

- BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA

**Version 3.6.1+galaxy1 - 05/04/2020**

- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0

- BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"

@HELP_XCMS_NEWVERSION_3610@

@HELP_XCMS_NEWVERSION_3440@

**Version 3.0.0.0 - 14/02/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods

- IMPROVEMENT: the tool now shows all the parameters and not only those which were set.


**Version 1.0.4 - 13/02/2018**

- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0


**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>