--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aplcms_unsupervised.xml	Sun Oct 18 10:35:33 2020 +0000
@@ -0,0 +1,67 @@
+<tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy1">
+    <macros>
+        <import>aplcms_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command detect_errors="aggressive"><![CDATA[
+        #set file_str = str('", "').join([str($f) for $f in $files])
+
+        Rscript
+            -e 'x <- apLCMS::unsupervised(
+                    files = c("$file_str"),
+                    min_exp = $noise_filtering.min_exp,
+                    min_pres = $noise_filtering.min_pres,
+                    min_run = $noise_filtering.min_run,
+                    mz_tol = $noise_filtering.mz_tol,
+                    baseline_correct = $noise_filtering.baseline_correct,
+                    baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
+                    intensity_weighted = $noise_filtering.intensity_weighted,
+                    shape_model = "$feature_detection.shape_model",
+                    BIC_factor = $feature_detection.BIC_factor,
+                    peak_estim_method = "$feature_detection.peak_estim_method",
+                    min_bandwidth = $feature_detection.min_bandwidth,
+                    max_bandwidth = $feature_detection.max_bandwidth,
+                    sd_cut = c($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_chr_tol = $peak_alignment.align_chr_tol,
+                    align_mz_tol = $peak_alignment.align_mz_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 = $weak_signal_recovery.recover_min_count
+                )'
+            -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
+    ]]></command>
+
+    <expand macro="inputs">
+        <expand macro="noise_filtering" />
+        <expand macro="feature_detection" />
+        <expand macro="peak_alignment" />
+        <expand macro="weak_signal_recovery" />
+    </expand>
+
+    <outputs>
+        <data name="peaks" format="h5" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
+            <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/>
+        </test>
+    </tests>
+
+    <help>
+        This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
+        any historically detected features. For such functionality please use the Hybrid version of apLCMS.
+
+        @GENERAL_HELP@
+    </help>
+
+    <expand macro="citations" />
+</tool>