--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/decontaminator.xml	Mon Jan 09 13:27:09 2023 +0000
@@ -0,0 +1,49 @@
+<tool id="decontaminator" name="decontaminator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">decontaminator</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir -p '${predicted_fragments.extra_files_path}' &&
+    python '$__tool_directory__/predict.py'
+        --test_ds '${fasta_file}'
+        --weights '${weights.fields.path}'
+        --out_path '${predicted_fragments.extra_files_path}'
+        --return_viral True
+    && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv
+    && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv
+    && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta
+
+    ]]></command>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>
+        <param name="weights" type="select" label="Select a reference model" help="If your model of interest is not listed, contact the Galaxy team">
+            <options from_data_table="decontaminator_models">
+                <validator type="no_options" message="No models are available for the selected input dataset" />
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/>
+        <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/>
+        <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_file" value="viruses.fasta"/>
+            <param name="weights" value="test"/>
+            <output name="predicted_fragments" file="predicted_fragments.tsv"  ftype="tabular" lines_diff="2"/>
+            <output name="predicted" file="predicted.tsv"  ftype="tabular" lines_diff="2"/>
+            <output name="viral" file="viral.fasta"  ftype="fasta" lines_diff="2"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+    Decontaminator is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in
+    sequening datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host and bacterial (contamination).
+ ]]></help>
+</tool>