--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_aplcms_two_step_hybrid.xml	Thu May 26 16:47:09 2022 +0000
@@ -0,0 +1,111 @@
+<tool id="recetox_aplcms_two_step_hybrid" name="RECETOX apLCMS Two-Step Hybrid" version="@TOOL_VERSION@+galaxy0">
+    <description>generate a feature table from LC/MS spectra of multi-batch experiments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator">
+        <person
+            givenName="Maksym"
+            familyName="Skoryk"
+            url="https://github.com/maximskorik"
+            identifier="0000-0003-2056-8018" />
+    </expand>
+
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        sh ${symlink_inputs} &&
+        Rscript  -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
+    ]]></command>
+    <configfiles>
+        <configfile name="symlink_inputs">
+            #for $infile in $files
+                ln -s '${infile}' '${infile.element_identifier}'
+            #end for
+        </configfile>
+        <configfile name="run_script"><![CDATA[
+            #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
+
+            two_step_hybrid_main(
+                sample_files = c('$filenames_str'),
+                known_table_file = '${known_table}',
+                updated_known_table_file = '${updated_known_table}',
+                recovered_file = '${recovered_feature_sample_table}',
+                aligned_file = '${aligned_feature_sample_table}',
+                out_format = '$output_format.out_format',
+                metadata = '${metadata}',
+                cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)),
+                min.within.batch.prop.detect = $multibatch_processing.min_within_batch_prop_detect,
+                min.within.batch.prop.report = $multibatch_processing.min_within_batch_prop_detect,
+                min.batch.prop = $multibatch_processing.min_batch_prop,
+                batch.align.mz.tol = $multibatch_processing.batch_align_mz_tol,
+                batch.align.chr.tol = $multibatch_processing.batch_align_chr_tol,
+                min.pres = $noise_filtering.min_pres,
+                min.run = $noise_filtering.min_run,
+                mz.tol = $noise_filtering.mz_tol,
+                baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
+                baseline.correct = $noise_filtering.baseline_correct,
+                intensity.weighted = $noise_filtering.intensity_weighted,
+                shape.model = '$feature_detection.shape_model',
+                peak.estim.method = '$feature_detection.peak_estim_method',
+                BIC.factor = $feature_detection.BIC_factor,
+                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),
+                component.eliminate = $feature_detection.component_eliminate,
+                moment.power = $feature_detection.moment_power,
+                align.mz.tol = $peak_alignment.align_mz_tol,
+                align.chr.tol = $peak_alignment.align_chr_tol,
+                max.align.mz.diff = $peak_alignment.max_align_mz_diff,
+                recover.mz.range = $weak_signal_recovery.recover_mz_range,
+                recover.chr.range = $weak_signal_recovery.recover_chr_range,
+                use.observed.range = $weak_signal_recovery.use_observed_range,
+                recover.min.count = $weak_signal_recovery.recover_min_count,
+                match.tol.ppm = $history_db.match_tol_ppm,
+                new.feature.min.count = $history_db.new_feature_min_count
+            )
+        ]]></configfile>
+    </configfiles>
+
+    <expand macro="inputs">
+        <param name="metadata" type="data" format="csv" label="metadata" help="A csv table with two columns, where the first column contains sample names and the second batch labels for each sample."/>
+        <expand macro="history_db"/>
+        <expand macro="noise_filtering" />
+        <expand macro="feature_detection"/>
+        <expand macro="peak_alignment"/>
+        <expand macro="weak_signal_recovery"/>
+        <expand macro="multibatch_processing"/>
+        <expand macro="output_format"/>
+    </expand>
+
+    <outputs>
+        <expand macro="unsupervised_outputs"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="known_table" value="known_table.parquet" ftype="parquet"/>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml,mbr_test0_copy.mzml" ftype="mzml"/>
+            <param name="metadata" value="two_step_hybrid_info.csv" ftype="csv"/>
+            <param name="moment_power" value="2"/>
+            <param name="sd_cut_max" value="100"/>
+            <param name="sd_cut_min" value="0.1"/>
+            <param name="sigma_ratio_lim_max" value="20"/>
+            <param name="sigma_ratio_lim_min" value="0.05"/>
+            <section name="output_format">
+                <param name="out_format" value="recetox"/>
+            </section>
+            <output name="recovered_feature_sample_table" file="two_step_hybrid.recetox.parquet" ftype="parquet"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            @HELP_two-step-hybrid@
+        ]]>
+    </help>
+
+    <expand macro="citations">
+        <citation type="doi">10.1038/s41598-020-70850-0</citation>
+    </expand>
+</tool>