<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.5">

    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>

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

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

    <command><![CDATA[
        @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r
        image_pos '$image_pos'
        image_neg '$image_neg'

        pos $pos tol
        $tol ruleset
        $ruleset keep_meta
        $keep_meta

        convertRTMinute $export.convertRTMinute
        numDigitsMZ $export.numDigitsMZ
        numDigitsRT $export.numDigitsRT

    ]]></command>

    <inputs>
        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />

        <param name="pos" type="select" label="Returned peaklist polarity mode">
            <option value="TRUE" selected="true">positive</option>
            <option value="FALSE" >negative</option>
        </param>

        <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
        <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
        <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>

        <section name="export" title="Export options">
            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
        </section>
    </inputs>

    <outputs>
        <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
        <!--
        <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" />
        -->
    </outputs>

    <tests>
        <test>
            <!-- TODO: generer des vrais dataset pos et neg-->
            <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
            <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
            <param name="pos" value="TRUE"/>
            <param name="tol" value="2"/>
            <param name="ruleset" value="1,1"/>
            <section name="export">
                <param name="convertRTMinute" value="True"/>
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </section>
            <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
        </test>
    </tests>


    <help><![CDATA[

@HELP_AUTHORS@

=======================
Xcms.combinexsAnnos
=======================

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

**What it does?**

This function check annotations of ion species with the help of a sample from opposite ion mode.
As first step it searches for pseudospectra from the positive and the negative sample within a reten-
tion time window. For every result the m/z differences between both samples are matched against
specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
mode with recalculated annotations.

**Details**

Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
tation the resulting peaklist only includes annotation with matches peaks from both mode according
to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and
xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!



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


**Upstream tools**

========================= ======================= ===================== ==========
Name                      Output file             Format                Parameter
========================= ======================= ===================== ==========
xcms.annotatediffreport   xset.annotate_POS.RData rdata.camera.positive RData file
------------------------- ----------------------- --------------------- ----------
xcms.annotatediffreport   xset.annotate_NEG.RData rdata.camera.positive RData file
========================= ======================= ===================== ==========

**Downstream tools**

+---------------------------+-----------------------------------------+--------+
| Name                      | Output file                             | Format |
+===========================+=========================================+========+
|Batch_correction           |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
+---------------------------+-----------------------------------------+--------+
|Filters                    |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
+---------------------------+-----------------------------------------+--------+
|Univariate                 |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
+---------------------------+-----------------------------------------+--------+
|Multivariate               |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
+---------------------------+-----------------------------------------+--------+



The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:
    | Batch_correction
    | Filters
    | Univariate
    | Multivariate PCA, PLS and OPLS


**Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow**

.. image:: combinexsannos_workflow_zoom.png

**General schema of the metabolomic workflow**

.. image:: combinexsannos_workflow.png


-----------
Input files
-----------

+---------------------------+----------------------------+
| Parameter : label         |   Format                   |
+===========================+============================+
| Positive RData ion mode   |   rdata.camera.positive    |
+---------------------------+----------------------------+
| Negative RData ion mode   |   rdata.camera.negative    |
+---------------------------+----------------------------+

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

xset.combinexsAnnos.variableMetadata.tsv

    | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
    | For each metabolite (row) :
    | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode

xset.combinexsAnnos.Rdata

    | Rdata file, that be used outside Galaxy in R.


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

---------------
Working example
---------------

Input files
-----------

    | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
    | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**

Parameters
----------

    | pos -> **positive**
    | tol -> **2 (default)**
    | ruleset -> **1,1 (default)**

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

**Example of an xset.combinexsAnnos.variableMetadata.tsv output:**

.. image:: combinexsannos_variableMetadata.png


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

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

.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS

**Version 2.2.5 - 09/04/2019**

- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)

- UPGRADE: refactoring of internal code

**Version 2.2.2 - 01/03/2018**

- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0

**Version 2.0.7 - 29/11/2017**

- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C


**Version 2.0.6 - 10/02/2017**

- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)


**Version 2.0.5 - 22/12/2016**

- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)

**Version 2.0.4 - 21/04/2016**

- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0


**Version 2.0.3 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs


**Version 2.0.1 - 07/06/2015**

- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.


**Version 2.0.0 - 09/06/2015**

- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode


    ]]></help>

    <expand macro="citation" />


</tool>