# HG changeset patch
# User recetox
# Date 1686837708 0
# Node ID 050cfef6ba65b5885a8b1790a4f3d159e27b083d
# Parent  2ec9253a647e337944c4a8fcd278e55d7e677b28
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed

diff -r 2ec9253a647e -r 050cfef6ba65 macros.xml
--- a/macros.xml	Tue Sep 20 14:43:56 2022 +0000
+++ b/macros.xml	Thu Jun 15 14:01:48 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.2.4</token>
+    <token name="@TOOL_VERSION@">1.3.0</token>
 
     <xml name="creator">
         <creator>
@@ -23,6 +23,11 @@
                 familyName="Čech"
                 url="https://github.com/martenson"
                 identifier="0000-0002-9318-1781" />
+            <person
+                givenName="Zargham"
+                familyName="Ahmad"
+                url="https://github.com/zargham-ahmad"
+                identifier="0000-0002-6096-224X" />
             <organization
                 url="https://www.recetox.muni.cz/"
                 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
@@ -36,6 +41,8 @@
                    help="Features as columns, rows as samples. Column header in format mz_rt."/>
             <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"
                    help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>
+            <param label="phenoData" name="csv_phenoData" type="data" format="csv" optional="true"
+                   help="Optional csv containing phenoData."/>
         </section>
     </xml>
 
@@ -43,8 +50,17 @@
         <section name="xcms" title="Input MS Data as XCMS" expanded="true">
             <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"
                    help="Grouped feature data for clustering." />
-            <param label="Preserve phenotype" name="usePheno" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
-                   help="Transfer phenotype data from XCMS object to Spec abundance file."/>
+        </section>
+    </xml>
+
+    <xml name="parameters_recetox_aplcms">
+        <section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
+            <param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet"
+                   help="Metadata with columns: mz, rt, feature names containing MS data."/>
+            <param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet"
+                   help="data with rownames = sample names, colnames = feature names containing MS data."/>
+            <param label="phenoData" name="df_phenoData" type="data" format="tsv,csv" optional="true"
+                   help="CSV/TSV file containing phenoData (optional)."/>
         </section>
     </xml>
 
@@ -53,7 +69,6 @@
         <param label="Correlation method" name="cor_method" type="select" display="radio"
                help="Choose correlational method to be used - see [1] for details.">
             <option value="pearson" selected="true">pearson</option>
-            <option value="everything">everything</option>
             <option value="spearman">spearman</option>
             <option value="kendall">kendall</option>
         </param>
@@ -90,9 +105,10 @@
                     <option value="TIC">TIC</option>
                     <option value="quantile">quantile</option>
                     <option value="batch.qc">batch.qc</option>
+                    <option value="qc">qc</option>
                 </param>
                 <when value="batch.qc">
-                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
+                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv"
                            help="CSV with sample names (or indices, currently not handled) on rows and columns with:
                            batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
                            ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
@@ -105,6 +121,25 @@
                              detection), while wider values provide less local precision in normalization but better
                              stability to individual peak areas."/>
                 </when>
+                <when value="qc">
+                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
+                           help="CSV with sample names (or indices, currently not handled) on rows and columns with:
+                           batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
+                           ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
+                    <param label="p.cut" name="p_cut" type="float" value="0.05" 
+                            help="Numeric when run order correction is applied, only features showing a run order vs 
+                            signal with a linear p-value (after FDR correction) &lt; p.cut will be adjusted.  also requires 
+                            r-squared &lt; rsq.cut."/>
+                    <param label="rsq.cut" name="rsq_cut" type="float" value="0.1" 
+                            help="Numeric when run order correction is applied, only features showing a run order vs signal 
+                            with a linear r-squared &gt; rsq.cut will be adjusted. also requires p values &lt; p.cut."/>
+                    <param label="p.adjust" name="p_adjust" type="text" value="none" 
+                            help="Which p-value adjustment should be used? one of ['holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 
+                            'BY', 'fdr', 'none']"/>
+                </when>
+                <when value="none"/>
+                <when value="TIC"/>
+                <when value="quantile"/>
             </conditional>
         </section>
 
@@ -143,7 +178,7 @@
     </xml>
 
     <xml name="output_msp">
-       <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_collection" type="list">
+       <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list">
            <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
            <filter>not msp_output_details['merge_msp']</filter>
        </collection>
diff -r 2ec9253a647e -r 050cfef6ba65 ramclustr.xml
--- a/ramclustr.xml	Tue Sep 20 14:43:56 2022 +0000
+++ b/ramclustr.xml	Thu Jun 15 14:01:48 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
     <macros>
         <import>macros.xml</import>
@@ -7,10 +7,11 @@
 
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
+        <requirement type="package" version="3.20.0">bioconductor-xcms</requirement>
+        <requirement type="package" version="9.0.0">r-arrow</requirement>
     </requirements>
 
-    <command detect_errors="aggressive"><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         Rscript
             -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
             -e 'source("${ramclustr_method}")'
@@ -18,52 +19,94 @@
     </command>
     <configfiles>
         <configfile name="ramclustr_method">
-            store_output(
-                #if $filetype.type_choice == "xcms":
-                ramclustr_xcms(
-                    input_xcms = "$filetype.xcms.input_xcms",
-                    use_pheno = $filetype.xcms.usePheno,
-                #else:
-                ramclustr_csv(
-                    ms = "$filetype.ms_csv.ms",
+            #if $filetype.type_choice == "xcms":
+            obj = load("$filetype.xcms.input_xcms")
+            ramclustObj = RAMClustR::rc.get.xcms.data(
+                xcmsObj = xdata,
+                #if $extras.ExpDes:
+                    ExpDes = load_experiment_definition("${$extras.ExpDes}"),
+                #end if
+                mzdec = $msp_output_details.mzdec,
+                ensure.no.na = $extras.replace_zeros
+            )
+            #else if $filetype.type_choice == "csv":
+            ramclustObj = RAMClustR::rc.get.csv.data(
+                csv = "$filetype.ms_csv.ms",
+                #if $filetype.ms_csv.idmsms:
                     idmsms = "$filetype.ms_csv.idmsms",
                 #end if
-                    sr = $filetype.required.sr,
-                    #if $filetype.type_choice == "xcms":
-                        #if $filetype.required.st
-                            st = $filetype.required.st,
-                        #end if
-                    #else:
-                        st = $filetype.required.st,
-                    #end if
-                    cor_method = "$filetype.required.cor_method",
-                    maxt = $filetype.required.maxt,
-                    linkage = "$clustering.linkage",
-                    min_module_size = $clustering.minModuleSize,
-                    hmax = $clustering.hmax,
-                    deep_split = "$clustering.deepSplit",
-                    normalize = "$normalisation.normalisation_method.normalize",
-                    #if "$normalisation.normalisation_method.normalize" == "batch.qc":
-                        metadata_file = "$normalisation.normalisation_method.batch_order_qc",
-                        qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
-                    #end if
-                    block_size = $performance.blocksize,
-                    mult = $performance.mult,
-                    mzdec = $msp_output_details.mzdec,
-                    rt_only_low_n = $extras.rt_only_low_n,
-                    replace_zeros = $extras.replace_zeros,
-                    #if $extras.ExpDes:
-                        exp_design = "${$extras.ExpDes}"
-                    #end if
-                ),
-                $msp_output_details.merge_msp,
-                "$spec_abundance",
-            #if $msp_output_details.merge_msp:
-                "$mass_spectra_merged"
-            #else:
-                NULL
+                #if $filetype.ms_csv.csv_phenoData:
+                    phenoData = "$filetype.ms_csv.csv_phenoData",
+                #end if
+                #if $extras.ExpDes:
+                    ExpDes = load_experiment_definition("${$extras.ExpDes}"),
+                #end if
+                st = $filetype.required.st,
+                ensure.no.na = $extras.replace_zeros
+            )
+            #else if $filetype.type_choice == "recetox-aplcms":
+            ramclustObj = read_ramclustr_aplcms(
+                ms1_featuredefinitions = "$filetype.ms_dataframe.ms1_featureDefinitions",
+                ms1_featurevalues = "$filetype.ms_dataframe.ms1_featureValues",
+                #if $filetype.ms_dataframe.df_phenoData:
+                    df_phenodata = "$filetype.ms_dataframe.df_phenoData",
+                    phenodata_ext = "${filetype.ms_dataframe.df_phenoData.ext}",
+                #end if
+                #if $extras.ExpDes:
+                    exp_des = "${$extras.ExpDes}",
+                #end if
+                st = $filetype.required.st,
+                ensure_no_na = $extras.replace_zeros
+            )
+            #end if
+
+            #if $extras.replace_zeros == "TRUE":
+            ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
             #end if
-                )
+
+            #if $normalisation.normalisation_method.normalize != "none":
+            ramclustObj = apply_normalisation(
+                ramclustr_obj = ramclustObj,
+                #if $normalisation.normalisation_method.normalize == "batch.qc":
+                    metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
+                    qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
+                #end if
+                #if $normalisation.normalisation_method.normalize == "qc":
+                    metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
+                    p_cut = $normalisation.normalisation_method.p_cut,
+                    rsq_cut = $normalisation.normalisation_method.rsq_cut,
+                    p_adjust = $normalisation.normalisation_method.p_adjust,
+                #end if
+                normalize_method = "$normalisation.normalisation_method.normalize"
+            )
+            #end if
+
+            ramclustObj = RAMClustR::rc.ramclustr(
+                ramclustObj = ramclustObj,
+                st = $filetype.required.st,
+                sr = $filetype.required.sr,
+                maxt = $filetype.required.maxt,
+                deepSplit = $clustering.deepSplit,
+                blocksize = $performance.blocksize,
+                mult = $performance.mult,
+                hmax = $clustering.hmax,
+                minModuleSize = $clustering.minModuleSize,
+                linkage = "$clustering.linkage",
+                cor.method = "$filetype.required.cor_method",
+                rt.only.low.n = $extras.rt_only_low_n,
+                fftempdir = NULL,
+            )
+            
+            store_output(
+                ramclustr_obj = ramclustObj,
+                output_merge_msp = $msp_output_details.merge_msp,
+                output_spec_abundance = "$spec_abundance",
+                #if $msp_output_details.merge_msp:
+                    msp_file = "$mass_spectra_merged"
+                #else:
+                    msp_file = NULL
+                #end if
+            )
         </configfile>
     </configfiles>
     <inputs>
@@ -71,6 +114,7 @@
             <param name="type_choice" type="select" label="Choose input format:">
                 <option value="xcms" selected="true">XCMS</option>
                 <option value="csv">CSV</option>
+                <option value="recetox-aplcms">RECETOX-APLCMS</option>
             </param>
             <when value="xcms">
                 <expand macro="parameters_xcms" />
@@ -88,6 +132,14 @@
                     <expand macro="parameters_required" />
                 </section>
             </when>
+            <when value="recetox-aplcms">
+                <expand macro="parameters_recetox_aplcms" />
+                <section name="required" title="General parameters" expanded="true">
+                    <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
+                           A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
+                    <expand macro="parameters_required" />
+                </section>
+            </when>
         </conditional>
         <expand macro="main_parameters" />
     </inputs>
@@ -108,6 +160,9 @@
                     <param name="maxt" value="259.8"/>
                 </section>
             </section>
+            <section name="msp_output_details">
+                <param name="mzdec" value="4"/>
+            </section>
             <section name="extras">
                 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
             </section>
@@ -124,12 +179,15 @@
                     <param name="maxt" value="78.4"/>
                 </section>
             </section>
+            <section name="msp_output_details">
+                <param name="mzdec" value="4"/>
+            </section>
             <section name="normalisation">
                 <section name="normalisation_method">
                     <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
                 </section>
             </section>
-            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/>
+            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
             <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
         </test>
         <test><!-- TEST 3 -->
@@ -159,6 +217,16 @@
             </section>
             <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
         </test>
+        <test><!-- TEST 5 -->
+            <section name="filetype">
+                <param name="type_choice" value="recetox-aplcms"/>
+                <section name="ms_dataframe">
+                    <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
+                    <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
+                </section>
+            </section>
+            <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
+        </test>
     </tests>
 
     <help>
diff -r 2ec9253a647e -r 050cfef6ba65 ramclustr_wrapper.R
--- a/ramclustr_wrapper.R	Tue Sep 20 14:43:56 2022 +0000
+++ b/ramclustr_wrapper.R	Thu Jun 15 14:01:48 2023 +0000
@@ -3,10 +3,15 @@
                          output_spec_abundance,
                          msp_file) {
     RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
-    write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE, quote = FALSE)
+    write.csv(ramclustr_obj$SpecAbund,
+        file = output_spec_abundance,
+        row.names = TRUE, quote = FALSE
+    )
 
     if (!is.null(msp_file)) {
-        exp_name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1]
+        exp_name <- ramclustr_obj$ExpDes[[1]][which(
+            row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"
+        ), 1]
         filename <- paste("spectra/", exp_name, ".msp", sep = "")
         file.copy(from = filename, to = msp_file, overwrite = TRUE)
     }
@@ -35,136 +40,100 @@
     return(data)
 }
 
-ramclustr_xcms <- function(input_xcms,
-                           use_pheno,
-                           sr,
-                           st = NULL,
-                           cor_method,
-                           maxt,
-                           linkage,
-                           min_module_size,
-                           hmax,
-                           deep_split,
-                           normalize,
-                           metadata_file = NULL,
-                           qc_inj_range,
-                           block_size,
-                           mult,
-                           mzdec,
-                           rt_only_low_n,
-                           replace_zeros,
-                           exp_design = NULL) {
-    obj <- load(input_xcms)
+read_ramclustr_aplcms <- function(ms1_featuredefinitions = NULL,
+                                  ms1_featurevalues = NULL,
+                                  df_phenodata = NULL,
+                                  phenodata_ext = NULL,
+                                  exp_des = NULL,
+                                  st = NULL,
+                                  ensure_no_na = TRUE) {
+    ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
+    ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
 
+    if (!is.null(df_phenodata)) {
+        if (phenodata_ext == "csv") {
+            df_phenodata <- read.csv(
+                file = df_phenodata,
+                header = TRUE, check.names = FALSE
+            )
+        } else {
+            df_phenodata <- read.csv(
+                file = df_phenodata,
+                header = TRUE, check.names = FALSE, sep = "\t"
+            )
+        }
+    }
+    if (!is.null(exp_des)) {
+        exp_des <- load_experiment_definition(exp_des)
+    }
+
+    feature_values <- ms1_featurevalues[-1]
+    feature_values <- t(feature_values)
+    colnames(feature_values) <- ms1_featurevalues[[1]]
+
+    feature_definitions <- data.frame(ms1_featuredefinitions)
+
+    ramclustr_obj <- RAMClustR::rc.get.df.data(
+        ms1_featureDefinitions = feature_definitions,
+        ms1_featureValues = feature_values,
+        phenoData = df_phenodata,
+        ExpDes = exp_des,
+        st = st,
+        ensure.no.na = ensure_no_na
+    )
+    return(ramclustr_obj)
+}
+
+apply_normalisation <- function(ramclustr_obj = NULL,
+                                normalize_method,
+                                metadata_file = NULL,
+                                qc_inj_range,
+                                p_cut,
+                                rsq_cut,
+                                p_adjust) {
     batch <- NULL
     order <- NULL
     qc <- NULL
 
-    if (!is.null(metadata_file)) {
-        metadata <- read_metadata(metadata_file)
-        batch <- metadata$batch
-        order <- metadata$order
-        qc <- metadata$qc
-    }
-
-    experiment <- NULL
-
-    if (!is.null(exp_design)) {
-        experiment <- load_experiment_definition(exp_design)
-    }
-
-    x <- RAMClustR::ramclustR(
-        xcmsObj = xdata,
-        st = st,
-        maxt = maxt,
-        sr = sr,
-        deepSplit = deep_split,
-        blocksize = block_size,
-        mult = mult,
-        hmax = hmax,
-        usePheno = use_pheno,
-        mspout = FALSE,
-        qc.inj.range = qc_inj_range,
-        normalize = normalize,
-        minModuleSize = min_module_size,
-        linkage = linkage,
-        mzdec = mzdec,
-        cor.method = cor_method,
-        rt.only.low.n = rt_only_low_n,
-        fftempdir = NULL,
-        replace.zeros = replace_zeros,
-        batch = batch,
-        order = order,
-        qc = qc,
-        ExpDes = experiment
-    )
-    return(x)
-}
+    if (normalize_method == "TIC") {
+        ramclustr_obj <- RAMClustR::rc.feature.normalize.tic(
+            ramclustObj =
+                ramclustr_obj
+        )
+    } else if (normalize_method == "quantile") {
+        ramclustr_obj <- RAMClustR::rc.feature.normalize.quantile(ramclustr_obj)
+    } else if (normalize_method == "batch.qc") {
+        if (!(is.null(metadata_file) || metadata_file == "None")) {
+            metadata <- read_metadata(metadata_file)
+            batch <- metadata$batch
+            order <- metadata$order
+            qc <- metadata$qc
+        }
 
-ramclustr_csv <- function(ms,
-                          idmsms,
-                          sr,
-                          st,
-                          cor_method,
-                          maxt,
-                          linkage,
-                          min_module_size,
-                          hmax,
-                          deep_split,
-                          normalize,
-                          metadata_file = NULL,
-                          qc_inj_range,
-                          block_size,
-                          mult,
-                          mzdec,
-                          rt_only_low_n,
-                          replace_zeros,
-                          exp_design = NULL) {
-    if (!file.exists(idmsms)) {
-        idmsms <- NULL
-    }
-
-    batch <- NULL
-    order <- NULL
-    qc <- NULL
-
-    if (!is.null(metadata_file)) {
-        metadata <- read_metadata(metadata_file)
-        batch <- metadata$batch
-        order <- metadata$order
-        qc <- metadata$qc
-    }
+        ramclustr_obj <- RAMClustR::rc.feature.normalize.batch.qc(
+            order = order,
+            batch = batch,
+            qc = qc,
+            ramclustObj = ramclustr_obj,
+            qc.inj.range = qc_inj_range
+        )
+    } else {
+        if (!(is.null(metadata_file) || metadata_file == "None")) {
+            metadata <- read_metadata(metadata_file)
+            batch <- metadata$batch
+            order <- metadata$order
+            qc <- metadata$qc
+        }
 
-    experiment <- NULL
-
-    if (!is.null(exp_design)) {
-        experiment <- load_experiment_definition(exp_design)
+        ramclustr_obj <- RAMClustR::rc.feature.normalize.qc(
+            order = order,
+            batch = batch,
+            qc = qc,
+            ramclustObj = ramclustr_obj,
+            p.cut = p_cut,
+            rsq.cut = rsq_cut,
+            p.adjust = p_adjust
+        )
     }
-
-    x <- RAMClustR::ramclustR(
-        ms = ms,
-        idmsms = idmsms,
-        st = st,
-        maxt = maxt,
-        sr = sr,
-        deepSplit = deep_split,
-        blocksize = block_size,
-        mult = mult,
-        hmax = hmax,
-        mspout = FALSE,
-        qc.inj.range = qc_inj_range,
-        normalize = normalize,
-        minModuleSize = min_module_size,
-        linkage = linkage,
-        mzdec = mzdec,
-        cor.method = cor_method,
-        rt.only.low.n = rt_only_low_n,
-        fftempdir = NULL,
-        replace.zeros = replace_zeros,
-        batch = batch,
-        order = order,
-        qc = qc,
-        ExpDes = experiment
-    )
-    return(x)
+    return(ramclustr_obj)
 }
diff -r 2ec9253a647e -r 050cfef6ba65 test-data/test5_df_featureDefinitions_input.parquet
Binary file test-data/test5_df_featureDefinitions_input.parquet has changed
diff -r 2ec9253a647e -r 050cfef6ba65 test-data/test5_df_featureValues_input.parquet
Binary file test-data/test5_df_featureValues_input.parquet has changed
diff -r 2ec9253a647e -r 050cfef6ba65 test-data/test5_spec_abundance.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_spec_abundance.csv	Thu Jun 15 14:01:48 2023 +0000
@@ -0,0 +1,10 @@
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diff -r 2ec9253a647e -r 050cfef6ba65 test-data/test5_spectra.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_spectra.msp	Thu Jun 15 14:01:48 2023 +0000
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