--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_metaphlan_database.xml	Mon Feb 13 11:37:08 2023 +0000
@@ -0,0 +1,74 @@
+<tool id="extract_metaphlan_database" name="Extract the marker sequences and metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>from the MetaPhlAn4 database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <version_command>metaphlan -v</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+bowtie2-inspect
+    '${cached_db.fields.path}/${cached_db.fields.dbkey}'
+    > '$sequences'
+
+&&
+
+python '$__tool_directory__/customizemetadata.py'
+    transform_pkl_to_json
+    --pkl '${cached_db.fields.path}/${cached_db.fields.dbkey}.pkl'
+    --json '$metadata'
+    ]]></command>
+    <inputs>
+        <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
+            <options from_data_table="@IDX_DATA_TABLE@">
+                <filter type="static_value" column="4" value="@IDX_VERSION@"/>
+                <validator message="No MetaPhlAn database is available" type="no_options"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database"/>
+        <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="cached_db" value="test-db-20210409"/>
+            <output name="sequences" file="test-db.fasta" ftype="fasta" compare="sim_size">
+                <assert_contents>
+                    <has_line line=">13076__A0A2I1PE66__CYJ72_10760 UniRef90_A0A2I1PE66;k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis;GCA_002847845"/>
+                </assert_contents>
+            </output>
+            <output name="metadata" file="test-db.json" ftype="json" compare="sim_size">
+                <assert_contents>
+                    <has_text text="13076__A0A2I1PE66__CYJ72_10760"/>
+                    <has_text text="k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"/>
+                    <has_text text="GCA_002847845"/>
+                    <has_text text="clade"/>
+                    <has_text text="ext"/>
+                    <has_text text="len"/>
+                    <has_text text="taxon"/>
+                    <has_text text="markers"/>
+                    <has_text text="taxonomy"/>
+                    <has_text text="merged_taxon"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Reconstruct the marker sequences (in fasta format) and metadata (in JSON) from the MetaPhlAn BowTie2 database
+
+Outputs
+=======
+
+- Fasta file with marker sequences.
+
+    This file can be used to add new marker sequences and then customizing the database.
+
+- JSON file with marker metadata
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>