# HG changeset patch
# User iuc
# Date 1677481198 0
# Node ID e073891b2afcfd1134f67771ee788a70b3ff4919
# Parent  27250f92a01a98e3947e76485ef73c884af5fb5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2

diff -r 27250f92a01a -r e073891b2afc macros.xml
--- a/macros.xml	Sat Dec 03 10:42:15 2022 +0000
+++ b/macros.xml	Mon Feb 27 06:59:58 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 27250f92a01a -r e073891b2afc merge_metaphlan_tables.xml
--- a/merge_metaphlan_tables.xml	Sat Dec 03 10:42:15 2022 +0000
+++ b/merge_metaphlan_tables.xml	Mon Feb 27 06:59:58 2023 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
-    <version_command>merge_metaphlan_tables.py -v</version_command>
+    <version_command>metaphlan -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
 merge_metaphlan_tables.py
     #for $element in $inputs
@@ -15,20 +15,20 @@
 ]]>
     </command>
     <inputs>
-        <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn" />
+        <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn"/>
     </inputs>
     <outputs>
-        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
-            <output name="output" ftype="tabular" >
+            <output name="output" ftype="tabular">
                 <assert_contents>
                     <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
                     <has_text text="dataset_"/>
                     <has_text text="clade_name"/>
-                    <has_line_matching expression="#.*" />
+                    <has_line_matching expression="#.*"/>
                 </assert_contents>
             </output>
         </test>
diff -r 27250f92a01a -r e073891b2afc test-data/test_database.loc
--- a/test-data/test_database.loc	Sat Dec 03 10:42:15 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 27250f92a01a -r e073891b2afc 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 06:59:58 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 27250f92a01a -r e073891b2afc tool-data/metaphlan_database.loc.sample
--- a/tool-data/metaphlan_database.loc.sample	Sat Dec 03 10:42:15 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 27250f92a01a -r e073891b2afc 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 06:59:58 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 27250f92a01a -r e073891b2afc tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat Dec 03 10:42:15 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 27 06:59:58 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 27250f92a01a -r e073891b2afc tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Sat Dec 03 10:42:15 2022 +0000
+++ b/tool_data_table_conf.xml.test	Mon Feb 27 06:59:58 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>