--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jun 26 13:55:56 2023 +0000
@@ -0,0 +1,144 @@
+<macros>
+<token name="@TOOL_VERSION@">0.10.0</token>
+
+<xml name="requirements">
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">r-recetox-xmsannotator</requirement>
+    </requirements>
+</xml>
+
+<xml name="creator">
+    <creator>
+        <person
+            givenName="Jiří"
+            familyName="Novotný"
+            url="https://github.com/xtracko"
+            identifier="0000-0001-5449-3523" />
+        <person
+            givenName="Martin"
+            familyName="Čech"
+            url="https://github.com/martenson"
+            identifier="0000-0002-9318-1781" />
+        <person
+            givenName="Matej"
+            familyName="Troják"
+            url="https://github.com/xtrojak"
+            identifier="0000-0003-0841-2707" />
+        <organization
+            url="https://www.recetox.muni.cz/"
+            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+            name="RECETOX MUNI" />
+    </creator>
+</xml>
+
+<xml name="inputs">
+    <param name="metadata_table" type="data" format="parquet,csv">
+        <label>Metadata table</label>
+        <help><![CDATA[
+            Peak metadata table*.
+        ]]></help>
+    </param>
+    <param name="intensity_table" type="data" format="parquet,csv">
+        <label>Intensity table</label>
+        <help><![CDATA[
+            Table with intensities** for features (rows) across samples (columns).
+        ]]></help>
+    </param>
+    <param name="compound_table" type="data" format="parquet,csv">
+        <label>Compound database</label>
+        <help><![CDATA[
+            Database of compounds according to which the annotation is performed.
+            The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
+        ]]></help>
+    </param>
+    <param name="adduct_table" type="data" format="parquet,csv" optional="true">
+        <label>Adduct database</label>
+        <help><![CDATA[
+            Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
+            The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
+        ]]></help>
+    </param>
+    <param name="adduct_weights" type="data" format="parquet,csv" optional="true">
+        <label>Adduct weights</label>
+        <help>
+            A weight-by-adduct table.
+        </help>
+    </param>
+</xml>
+
+<xml name="outputs">
+    <data name="output_file" format="parquet">
+        <change_format>
+            <when input="metadata_table.ext" value="csv" format="csv" />
+        </change_format>
+    </data>
+</xml>
+
+<xml name="tolerance">
+    <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
+        <label>Mass tolerance [ppm]</label>
+        <help>Mass tolerance in ppm for database matching.</help>
+    </param>
+    <yield/>
+</xml>
+
+<token name="@HELP@">
+Description
+===========
+
+Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
+using advanced methods.
+
+The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
+peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
+withing some tolerance.
+
+Then, a score and a confidence level is assigned to each match based on peak correlation
+clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
+
+Input tables description
+------------------------
+
+(*) Metadata table
+~~~~~~~~~~~~~~~~~~
+
+The output from recetox-aplcms tool. 
+The `npeaks` column denotes the number of peaks which have been grouped into this feature. 
+The columns with the sample names indicate whether this feature is present in the sample.
+Only id, mz, and rt columns are required to be present.
+
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  id   | mz           |  mzmin       |  mzmax        |  rt            |  rtmin        |  rtmax        |   npeaks  |  21_qc_no_dil_milliq   |  29_qc_no_dil_milliq   |  8_qc_no_dil_milliq    |
++=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
+|  1    | 70.03707021  |  70.037066   |  70.0370750   |  294.1038014   |  294.0634942  |  294.149985   |   3       |  1                     |  1                     |  1                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  2    | 70.06505677  |  70.065045   |  70.0650676   |  141.9560055   |  140.5762528  |  143.335758   |   2       |  1                     |  0                     |  1                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  57   | 78.04643252  |  78.046429   |  78.0464325   |  294.0063397   |  293.9406777  |  294.072001   |   2       |  1                     |  1                     |  0                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  ...  | ...          |   ...        |  ...          |  ...           |  ...          |  ...          |   ...     |  ...                   |  ...                   |  ...                   |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+
+(**) Intensity table
+~~~~~~~~~~~~~~~~~~~~
+
+The output from recetox-aplcms tool.
+This table contains the peak area for aligned features in all samples.
+
++-------+------------------------+------------------------+------------------------+
+|  id   |  21_qc_no_dil_milliq   |  29_qc_no_dil_milliq   |  8_qc_no_dil_milliq    |
++=======+========================+========================+========================+
+|  1    |  13187487.20482895     |  7957395.699119729     |  11700594.397257797    |
++-------+------------------------+------------------------+------------------------+
+|  2    |  2075168.6398983458    |  0                     |  2574362.159289044     |
++-------+------------------------+------------------------+------------------------+
+|  57   |  2934524.4406785755    |  1333044.5065971944    |  0                     |
++-------+------------------------+------------------------+------------------------+
+|  ...  |  ...                   |  ...                   |  ...                   |
++-------+------------------------+------------------------+------------------------+
+</token>
+
+<xml name="citations">
+    <citation type="doi">10.1021/acs.analchem.6b01214</citation>
+</xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_xmsannotator_advanced.xml	Mon Jun 26 13:55:56 2023 +0000
@@ -0,0 +1,169 @@
+<tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy0">
+
+    <description>annotate peak intensity table including scores and confidence levels</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <xrefs>
+        <xref type="bio.tools">recetox-xmsannotator</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript -e 'source("${__tool_directory__}/utils.R")' -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')"
+    ]]></command>
+
+    <configfiles>
+        <configfile name="wrapper"><![CDATA[
+            metadata_table <- load_table("$metadata_table", "$metadata_table.ext")
+            intensity_table <- load_table("$intensity_table", "$intensity_table.ext")
+            peak_table <- create_peak_table(metadata_table, intensity_table)
+
+            filter_by <- create_filter_by_adducts("$filter_by")
+
+            annotation <- advanced_annotation(
+                peak_table = peak_table,
+                adduct_table = load_table("$adduct_table", "$adduct_table.ext"),
+                adduct_weights = load_table("$adduct_weights", "$adduct_weights.ext"),
+                compound_table = load_table("$compound_table", "$compound_table.ext"),
+                mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
+                time_tolerance = $time_tolerance,
+                correlation_threshold = as.double($clustering.correlation_threshold),
+                min_cluster_size = as.integer($clustering.min_cluster_size),
+                deep_split = as.integer($clustering.deep_split),
+                network_type = "$clustering.network_type",
+                redundancy_filtering = $scoring.redundancy_filtering,
+                n_workers = n_workers,
+                intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
+                mass_defect_tolerance = as.double($mass_defect_tolerance),
+                mass_defect_precision = as.double($mass_defect_precision),
+                peak_rt_width = as.integer($peak_rt_width),
+                maximum_isotopes = as.integer($maximum_isotopes),
+                min_ions_per_chemical = as.integer($min_ions_per_chemical),
+                filter_by = filter_by
+            )
+
+            save_table(annotation, "$output_file", "$output_file.ext")
+        ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="inputs"/>
+        <expand macro="tolerance">
+            <param name="time_tolerance" type="float" value="10" min="0">
+                <label>Retention time tolerance [s]</label>
+                <help>
+                    Retention time tolerance in seconds for finding peaks derived from the same parent compound.
+                </help>
+            </param>
+        </expand>
+        <section name="clustering" title="Clustering">
+            <param name="correlation_threshold" type="float" value="0.7">
+                <label>Correlation threshold</label>
+                <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
+            </param>
+            <param name="min_cluster_size" type="integer" value="10" min="1">
+                <label>Minimum cluster size</label>
+                <help>The minimum number of nodes to be considered as a cluster.</help>
+            </param>
+            <param name="deep_split" type="integer" value="2" min="0" max="4">
+                <label>Deep split</label>
+                <help>
+                    Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
+                    the more and smaller clusters will be produced (see WGCNA package documentation).
+                </help>
+            </param>
+            <param name="network_type" type="select" display="radio">
+                <label>Network type</label>
+                <help>
+                    Network type parameter affects how the network's adjacency matrix is created from the correlation
+                    matrix (see WGCNA package documentation).
+                </help>
+                <option value="signed">Signed</option>
+                <option value="unsigned" selected="true">Unsigned</option>
+            </param>
+        </section>
+        <section name="scoring" title="Scoring" expanded="true">
+            <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
+                <label>Strict boosting</label>
+                <help>
+                    Boost the scores of metabolites that not only belongs to the same pathway but also to the same
+                    cluster. Otherwise, do not account for cluster membership.
+                </help>
+            </param>
+            <param name="min_isp" type="integer" min="0" value="1">
+                <label>Minimum number of expected isotopes</label>
+                <help>
+                    Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
+                </help>
+            </param>
+            <param name="max_isp" type="integer" min="0" value="5">
+                <label>Maximum number of expected isotopes</label>
+                <help>
+                    Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
+                </help>
+            </param>
+            <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
+                <label>Redundancy filtering</label>
+                <help>Whether to filter out low-scored multiple matcher or not.</help>
+            </param>
+        </section>
+        <param name="intensity_deviation_tolerance" type="float" value="0.1">
+            <label>Tolerance of intensity deviation</label>
+            <help>A numeric threshold by which an intensity ratio of two isotopic peaks may differ from their actual abundance ratio.</help>
+        </param>
+        <param name="mass_defect_tolerance" type="float" value="0.1">
+            <label>Tolerance of mass defect</label>
+            <help>Maximum difference in mass defect between two peaks of the same compound.</help>
+        </param>
+        <param name="mass_defect_precision" type="float" value="0.01">
+            <label>Precision for computing mass defect</label>
+        </param>
+        <param name="peak_rt_width" type="integer" value="1">
+            <label>Estimated chromatographic peak width</label>
+        </param>
+        <param name="maximum_isotopes" type="integer" value="10">
+            <label>Maximum isotopes</label>
+        </param>
+        <param name="min_ions_per_chemical" type="integer" value="2">
+            <label>Minimum ions per chemical</label>
+        </param>
+        <param name="filter_by" type="select" label="Adducts to filter by" multiple="true" optional="true">
+            <option value="M-H" selected="true">M-H</option>
+            <option value="M+H" selected="true">M+H</option>
+            <option value="2M-H">2M-H</option>
+            <option value="M-2H">M-2H</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <expand macro="outputs"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="metadata_table" value="metadata_table.parquet" ftype="parquet" />
+            <param name="intensity_table" value="intensity_table.parquet" ftype="parquet" />
+            <param name="compound_table" value="database.parquet" ftype="parquet" />
+            <param name="adduct_table" value="adduct_table.parquet" ftype="parquet" />
+            <output name="output_file" file="expected_output.parquet" ftype="parquet"/>
+        </test>
+        <test>
+            <param name="metadata_table" value="metadata_table.csv" ftype="csv" />
+            <param name="intensity_table" value="intensity_table.csv" ftype="csv" />
+            <param name="compound_table" value="database.csv" ftype="csv" />
+            <param name="adduct_table" value="adduct_table.csv" ftype="csv" />
+            <output name="output_file" file="expected_output.csv" ftype="csv"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            @HELP@
+        ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations"/>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.R	Mon Jun 26 13:55:56 2023 +0000
@@ -0,0 +1,37 @@
+library(recetox.xmsannotator)
+library(dplyr)
+
+load_table <- function(filename, filetype) {
+    if (filename == "None") {
+        return(NULL)
+    }
+    if (filetype == "csv") {
+        return(as.data.frame(read.csv(filename)))
+    } else {
+        return(as.data.frame(arrow::read_parquet(filename)))
+    }
+}
+
+save_table <- function(table, filename, filetype) {
+    if (filetype == "csv") {
+        write.csv(table, filename, row.names = FALSE)
+    } else {
+        arrow::write_parquet(table, filename)
+    }
+}
+
+create_filter_by_adducts <- function(comma_separated_values) {
+    if (comma_separated_values == "None") {
+        return(NA)
+    }
+    filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]]
+    return(filter_by)
+}
+
+create_peak_table <- function(metadata_table, intensity_table) {
+    metadata_table <- select(metadata_table, id, mz, rt)
+    peak_table <- inner_join(metadata_table, intensity_table, by = "id")
+    peak_table <- rename(peak_table, peak = id)
+    peak_table$peak <- as.integer(peak_table$peak)
+    return(peak_table)
+}