annotate compound_identification.xml @ 2:caba07f41453 draft default tip

"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"

<tool id="secimtools_compound_identification" name="Compound Identification" version="@WRAPPER_VERSION@">
    <description>based on m/z ratio and retention time.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
compound_identification.py
--anno $anno
--uniqID $uniqID
--mzID $mzID
--rtID $rtID
--library $library
--libuniqID $libuniqID
--libmzID $libmzID
--librtID $librtID
--output $output
    ]]></command>
    <inputs>
        <param name="anno" type="data" format="tabular" label="Target Annotation File" help="Input tab-separated dataset in wide format. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" optional="false" label="Target Annotation Unique Feature ID column" help="Name of the column in your target annotation file containing unique identifiers."/>
        <param name="mzID" type="text" size="30" value="" optional="false" label="Target Annotation Mass/Charge column." help="Name of the column in your target annotation file containing m/z ratios."/>
        <param name="rtID" type="text" size="30" value="" optional="false" label="Target Annotation Retention Time" help="Name of the column in your target annotation file containing retention times."/>
        <param name="library" type="data" format="tabular" label="Library File" help="Library dataset. If not tab separated see TIP below."/>
        <param name="libuniqID" type="text" size="30" value="" optional="false" label="Library compound name column" help="Name of the column in your library file containing the compound/adduct names to use for identification."/>
        <param name="libmzID" type="text" size="30" value="" optional="false" label="Library Mass/Charge column" help="Name of the column in your library file containing m/z ratios."/>
        <param name="librtID" type="text" size="30" value="" optional="false" label="Library Retention Time column" help="Name of the column in your library file containing the retention times."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="identified_compounds_adducts_on_${anno.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="anno"      value="TEST0000_mzrt_first.tsv"/>
            <param name="uniqID"    value="rowID_first"/>
            <param name="mzID"      value="MZ_first" />
            <param name="rtID"      value="RT_first" />
            <param name="library"   value="TEST0000_database.tsv"/>
            <param name="libuniqID" value="name_database"/>
            <param name="libmzID"   value="MZ_database" />
            <param name="librtID"   value="RT_database" />
            <output name="output"   file="TEST0000_compound_identification_output.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

This tool is primarily intended for identification of compounds in a target file given a mass spectroscopy library file.

Each metabolite (feature) is characterized by a mass to charge (m/z) ratio and retention time (RT).

This tool matches two files: (1) a mass spectroscopy library file and (2) a target annotation file.

The library file (in tsv format) contains a list of compounds and their associated m/z ratios and RTs.

The target annotation file (in tsv format) contains the m/z ratios and RTs for the experimental samples.

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

**Input**

    - Two input datasets are required, a library file and an annotation target file.

@MZRTFILE@

**Target Annotation Unique Feature ID column**

    - Name of the column in your target annotation file containing unique ID.


**Annotation Mass/Charge column**

    - Name of the column in your target annotation file containing the m/z ratio.

**Annotation Retention Time**

    - Name of the column in your target annotation file containing Retention Times.

**Library File**

**Library compound name colum**

    - Name of the column in your library file containing the compound names to use.

**Library Mass/Charge column**

    - Name of the column in your library file containing the m/z ratios.

**Library Retention Time column**

    - Name of the column in your library file containing Retention Times.


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

**Output**

A TSV file containing the original target annotation input file plus an additional column containing the name of any compounds that were matched using the m/z ratio and RT.

]]></help>
    <expand macro="citations"/>
</tool>