Mercurial > repos > workflow4metabolomics > camera_findadducts

<tool id="CAMERA_findAdducts" name="CAMERA.findAdducts" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">

    <description>Annotate adducts</description>

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

    <expand macro="requirements"/>

    <required_files>
        <include type="literal" path="CAMERA_findAdducts.R"/>
        <include type="literal" path="lib.r"/>
    </required_files>

    <command detect_errors="exit_code"><![CDATA[
		@COMMAND_RSCRIPT@CAMERA_findAdducts.R
		image '$image'
		ppm $ppm
		mzabs $mzabs
		polarity $polarity

		#if $rules_block.rules_select == "FALSE":
            rules NULL
        #else
            rules $rules_block.rules
        #end if

        #if $advanced.advanced_select == "FALSE":
            multiplier 3
            max_peaks 100
            psg_list NULL
        #else
            multiplier $advanced.multiplier
            max_peaks $advanced.max_peaks
            #if $advanced.psg_list_block.psg_list_select == "FALSE":
                psg_list NULL
            #else
                psg_list $advanced.psg_list_block.psg_list
            #end if
        #end if

		intval $intval
		convertRTMinute $convertRTMinute
		numDigitsMZ $numDigitsMZ
		numDigitsRT $numDigitsRT

        @COMMAND_FILE_LOAD@
		]]>
    </command>
    <inputs>
        <param name="image" type="data" label="RData file" format="rdata" help="Output file from another function CAMERA (findIsotopes)" />
        <param name="ppm" type="integer" value="5" label="General ppm error" />
        <param name="mzabs" type="float" value="0.015" label="General absolute error in m/z" />
        <param name="polarity" type="select" label="Which polarity mode was used for measuring of the MS sample">
            <option value="positive">positive</option>
            <option value="negative" selected="true">negative</option>
        </param>

        <conditional name="rules_block">
            <param name="rules_select" type="select" label="Use a personal ruleset file">
                <option value="TRUE">TRUE</option>
                <option value="FALSE" selected="true">FALSE</option>
            </param>
            <when value="FALSE">
                <!--<param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />-->
            </when>
            <when value="TRUE">
                <param name="rules" type="data" format="csv" label="User defined ruleset" />
            </when>
        </conditional>

        <param name="intval" type="select" label="Choose intensity values">
            <option value="into" selected="true">into</option>
            <option value="maxo">maxo</option>
            <option value="intb">intb</option>
        </param>

        <conditional name="advanced">
            <param name="advanced_select" type="select" label="Advanced parameters">
                <option value="TRUE">TRUE</option>
                <option value="FALSE" selected="true">FALSE</option>
            </param>
            <when value="FALSE">
                <!--<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" />
                <param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" optional="true" />
                <param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
            </when>
            <when value="TRUE">
                <param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" />
                <param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" />

                <conditional name="psg_list_block">
                    <param name="psg_list_select" type="select" label="Use a personal psg_list">
                        <option value="TRUE">TRUE</option>
                        <option value="FALSE" selected="true">FALSE</option>
                    </param>
                    <when value="FALSE">
                        <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
                    </when>
                    <when value="TRUE">
                        <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
                    </when>
                </conditional>
            </when>
        </conditional>
        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
        <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
        <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
        <expand macro="input_file_load"/>
    </inputs>
    <outputs>
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findAdducts.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
        <data name="camera_findAdducts_rdata" format="rdata" label="${image.name[:-6]}.findAdducts.RData" from_work_dir="camera_findAdducts.RData" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.RData" />
            <!--<param name="ppm" value="5" />
            <param name="mzabs" value="0.015" />
            <param name="polarity" value="positive" />
            <param name="rules" value="NULL" />
            <param name="intval" value="into" />
            <param name="multiplier" value="3" />
            <param name="max_peaks" value="100" />
            <param name="psg_list" value="NULL" />-->
            <expand macro="test_file_load_faahKO_15"/>
            <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
            <output name="camera_findAdducts_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" compare="sim_size" delta="5000" />
        </test>
    </tests>
    <help><![CDATA[

===================
CAMERA.findAdducts
===================

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

.. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf

Annotate adducts (and fragments) for a `xsAnnotate` object. Returns a `xsAnnotate` object with annotated pseudospectra. Click on the link to see the "Reference Manual" : link_ .

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

---------
Arguments
---------

+--------------+-------------------------------------------------------------------+
| Variables    | Descriptions                                                      |
+==============+===================================================================+
| object       | the xsAnnotate object                                             |
+--------------+-------------------------------------------------------------------+
| ppm          | ppm error for the search                                          |
+--------------+-------------------------------------------------------------------+
| mzabs        | allowed variance for the search                                   |
+--------------+-------------------------------------------------------------------+
| multiplier   | highest number(n) of allowed clusterion [nM+ion]                  |
+--------------+-------------------------------------------------------------------+
| polarity     | Which polarity mode was used for measuring of the ms sample       |
+--------------+-------------------------------------------------------------------+
| rules        | personal ruleset or with NULL standard ruleset will be calculated |
+--------------+-------------------------------------------------------------------+
| max_peaks    | If run in parallel mode, this number defines how many peaks will  |
|              | be calculated in every thread                                     |
+--------------+-------------------------------------------------------------------+
| psg_list     | Vector of pseudospectra indices. The correlation analysis will be |
|              | only done for those groups                                        |
+--------------+-------------------------------------------------------------------+
| intval       | choose intensity values. Allowed values are into, maxo, intb      |
+--------------+-------------------------------------------------------------------+

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

------------------------------------------
General schema of the metabolomic workflow
------------------------------------------

.. image:: findAdducts.png

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

-------
Details
-------

Adducts (and fragments) are annotated for a `xsAnnotate` object. For every pseudospectra group, generated by `groupFWHM` and `groupCorr`, all possible Adducts are calculated and mapped to the peaks. If at least two adducts match, a possible molecule-mass for the group can be calculated. After the annotation, every mass hypothesis is checked against the charge of the calculated isotopes. It is recommended to call `findIsotopes()` before the annotation step.

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

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

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

@HELP_CAMERA_SUITE@

]]>    </help>

    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>
author	workflow4metabolomics
date	Sun, 24 Nov 2024 21:31:14 +0000
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