--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_aplcms_extract_features.xml	Fri Jun 10 10:17:01 2022 +0000
@@ -0,0 +1,81 @@
+<tool id="recetox_aplcms_extract_features" name="RECETOX apLCMS - extract features" version="@TOOL_VERSION@+galaxy0">
+    <description>extract features from LC/MS spectra</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_split.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
+    ]]></command>
+    <configfiles>
+        <configfile name="run_script"><![CDATA[
+            profile <- proc.cdf(
+                filename = "$file",
+                min.pres = $noise_filtering.min_pres,
+                min.run = $noise_filtering.min_run,
+                tol = $noise_filtering.mz_tol,
+                baseline.correct = $noise_filtering.baseline_correct,
+                baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
+                intensity.weighted = $noise_filtering.intensity_weighted,
+                do.plot = FALSE,
+                cache = FALSE
+            )
+
+            features <- prof.to.features(
+                a = profile,
+                min.bw = $feature_detection.min_bandwidth,
+                max.bw = $feature_detection.max_bandwidth,
+                sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
+                sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
+                shape.model = '$feature_detection.shape_model',
+                estim.method = '$feature_detection.peak_estim_method',
+                component.eliminate = $feature_detection.component_eliminate,
+                power = $feature_detection.moment_power,
+                BIC.factor = $feature_detection.BIC_factor,
+                do.plot = FALSE
+            )
+
+            df <- as.data.frame(features)
+            arrow::write_parquet(df, "$feature_sample_table")
+        ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="file" type="data" format="mzdata,mzml,mzxml,netcdf" label="Input file"
+               help="Mass spectrometry file for peak extraction." />
+        <expand macro="noise_filtering_split"/>
+        <expand macro="feature_detection"/>
+    </inputs>
+
+    <outputs>
+        <data name="feature_sample_table" format="parquet" label="${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="file" value="mbr_test0.mzml" ftype="mzml"/>
+            <output name="feature_sample_table" file="extracted_expected/extracted_0.parquet" ftype="parquet"/>
+        </test>
+        <test>
+            <param name="file" value="mbr_test1.mzml" ftype="mzml"/>
+            <output name="feature_sample_table" file="extracted_expected/extracted_1.parquet" ftype="parquet"/>
+        </test>
+        <test>
+            <param name="file" value="mbr_test2.mzml" ftype="mzml"/>
+            <output name="feature_sample_table" file="extracted_expected/extracted_2.parquet" ftype="parquet"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            This is a tool which runs apLCMS features extraction.
+
+            @GENERAL_HELP@
+        ]]>
+    </help>
+
+    <expand macro="citations"/>
+</tool>