# HG changeset patch
# User iuc
# Date 1677481260 0
# Node ID 2131d7dca4558e14925df2603323a376d529ddef
# Parent  6dee4abadccb89c1e31c5f0717211405d21c272a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2

diff -r 6dee4abadccb -r 2131d7dca455 macros.xml
--- a/macros.xml	Sat Dec 03 10:43:21 2022 +0000
+++ b/macros.xml	Mon Feb 27 07:01:00 2023 +0000
@@ -1,17 +1,16 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">4.0.3</token>
+    <token name="@TOOL_VERSION@">4.0.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">20.01</token>
+    <token name="@PROFILE@">22.05</token>
+    <!-- Metaphlan DB compatible with this version of Metaphlan
+    v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> 
+    <token name="@IDX_VERSION@">SGB</token>
+    <token name="@IDX_DATA_TABLE@">metaphlan_database_versioned</token>
     <xml name="edam_ontology">
-        <edam_topics>
-            <edam_topic>topic_3174</edam_topic>
-            <edam_topic>topic_0194</edam_topic>
-        </edam_topics>
-        <edam_operations>
-            <edam_operation>operation_2478</edam_operation>
-            <edam_operation>operation_0324</edam_operation>
-        </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">metaphlan</xref>
+    </xrefs>
     </xml>
     <xml name="requirements">
         <requirements>
diff -r 6dee4abadccb -r 2131d7dca455 metaphlan.xml
--- a/metaphlan.xml	Sat Dec 03 10:43:21 2022 +0000
+++ b/metaphlan.xml	Mon Feb 27 07:01:00 2023 +0000
@@ -263,15 +263,16 @@
                     <option value="history">From history</option>
                 </param>
                 <when value="cached">
-                    <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
-                        <options from_data_table="metaphlan_database">
-                            <validator message="No MetaPhlAn database is available" type="no_options" />
+                    <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
+                        <options from_data_table="@IDX_DATA_TABLE@">
+                            <filter type="static_value" column="4" value="@IDX_VERSION@"/>
+                            <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
                         </options>
                     </param>
                 </when>
                 <when value="history">
                     <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
-                    <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
+                    <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
                 </when>
             </conditional>
         </section>
@@ -435,6 +436,7 @@
                 </assert_contents>
             </output>
             <output_collection name="levels" type="list" >
+            
                 <element name="all" ftype="tabular">
                     <assert_contents>
                         <has_text text="class"/>
@@ -442,21 +444,6 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum_id"/>
-                        <not_has_text text="kingdom_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class_id"/>
@@ -465,14 +452,6 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order_id"/>
-                        <not_has_text text="class_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family_id"/>
@@ -489,6 +468,29 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order_id"/>
+                        <not_has_text text="class_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum_id"/>
+                        <not_has_text text="kingdom_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species_id"/>
@@ -588,21 +590,6 @@
                         <has_n_columns n="17"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom_id"/>
-                        <has_text text="Bacteria"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum_id"/>
-                        <not_has_text text="kingdom_id"/>
-                        <has_text text="Firmicutes"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class_id"/>
@@ -611,14 +598,6 @@
                         <has_n_columns n="3"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order_id"/>
-                        <not_has_text text="class_id"/>
-                        <has_text text="Propionibacteriales"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family_id"/>
@@ -635,6 +614,29 @@
                         <has_n_columns n="3"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom_id"/>
+                        <has_text text="Bacteria"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order_id"/>
+                        <not_has_text text="class_id"/>
+                        <has_text text="Propionibacteriales"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum_id"/>
+                        <not_has_text text="kingdom_id"/>
+                        <has_text text="Firmicutes"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species_id"/>
@@ -988,20 +990,6 @@
                         <has_n_columns n="9"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom"/>
-                        <has_text text="Bacteria"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum"/>
-                        <has_text text="Firmicutes"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class"/>
@@ -1009,13 +997,6 @@
                         <has_n_columns n="2"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order"/>
-                        <has_text text="Propionibacteriales"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family"/>
@@ -1030,6 +1011,27 @@
                         <has_n_columns n="2"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom"/>
+                        <has_text text="Bacteria"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order"/>
+                        <has_text text="Propionibacteriales"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum"/>
+                        <has_text text="Firmicutes"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species"/>
diff -r 6dee4abadccb -r 2131d7dca455 test-data/test_database.loc
--- a/test-data/test_database.loc	Sat Dec 03 10:43:21 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-# Tab separated with 4 columns:
-# - value (Galaxy records this in the Galaxy DB)
-# - name (Galaxy shows this in the UI)
-# - value (Galaxy records this in the Galaxy DB)
-# - path (folder name containing the Kraken DB)  
-test-db-20210409	"Test Database"	test-db	${__HERE__}/test-db
\ No newline at end of file
diff -r 6dee4abadccb -r 2131d7dca455 test-data/test_database_versioned.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database_versioned.loc	Mon Feb 27 07:01:00 2023 +0000
@@ -0,0 +1,7 @@
+# Tab separated with 5 columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - value (Galaxy records this in the Galaxy DB)
+# - path (folder name containing the Kraken DB)
+# - db version (whether it is SGB of Metaphlan v4 or not)
+test-db-20210409	"Test Database"	test-db	${__HERE__}/test-db	SGB
diff -r 6dee4abadccb -r 2131d7dca455 tool-data/metaphlan_database.loc.sample
--- a/tool-data/metaphlan_database.loc.sample	Sat Dec 03 10:43:21 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of metagenomics files.  
-#file has this format (white space characters are TAB characters)
-#02_16_2014	 MetaPhlAn2 clade-specific marker genes	db_v20	/path/to/data
\ No newline at end of file
diff -r 6dee4abadccb -r 2131d7dca455 tool-data/metaphlan_database_versioned.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan_database_versioned.loc.sample	Mon Feb 27 07:01:00 2023 +0000
@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters)
+#02_16_2014	 MetaPhlAn2 clade-specific marker genes	db_v20	/path/to/data	SGB_or_legacy
diff -r 6dee4abadccb -r 2131d7dca455 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat Dec 03 10:43:21 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 27 07:01:00 2023 +0000
@@ -1,6 +1,7 @@
+<?xml version="1.0"?>
 <tables>
-    <table name="metaphlan_database" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="tool-data/metaphlan_database.loc" />
+    <table name="metaphlan_database_versioned" comment_char="#">
+        <columns>value, name, dbkey, path, db_version</columns>
+        <file path="tool-data/metaphlan_database_versioned.loc"/>
     </table>
 </tables>
diff -r 6dee4abadccb -r 2131d7dca455 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Sat Dec 03 10:43:21 2022 +0000
+++ b/tool_data_table_conf.xml.test	Mon Feb 27 07:01:00 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
-    <table name="metaphlan_database" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="${__HERE__}/test-data/test_database.loc" />
+    <table name="metaphlan_database_versioned" comment_char="#">
+        <columns>value, name, dbkey, path, db_version</columns>
+        <file path="${__HERE__}/test-data/test_database_versioned.loc"/>
     </table>
-</tables>
\ No newline at end of file
+</tables>