# HG changeset patch
# User iuc
# Date 1722237278 0
# Node ID a755466eb47c7456d4a14c6b3df1675d92b00feb
# Parent  254cb00a578ff6cb06ba175db7f41525b154811a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05

diff -r 254cb00a578f -r a755466eb47c customize_metaphlan_database.xml
--- a/customize_metaphlan_database.xml	Tue Apr 30 09:08:54 2024 +0000
+++ b/customize_metaphlan_database.xml	Mon Jul 29 07:14:38 2024 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="requirements">
-        <requirement type="package" version="1.3">seqtk</requirement>
+        <requirement type="package" version="1.4">seqtk</requirement>
     </expand>
     <version_command>metaphlan -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 254cb00a578f -r a755466eb47c macros.xml
--- a/macros.xml	Tue Apr 30 09:08:54 2024 +0000
+++ b/macros.xml	Mon Jul 29 07:14:38 2024 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">4.0.6</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@TOOL_VERSION@">4.1.1</token>
+    <token name="@VERSION_SUFFIX@">0</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 --> 
@@ -23,4 +23,9 @@
             <citation type="doi">10.7554/eLife.65088</citation>
         </citations>
     </xml>
+
+    <xml name="subsample_common">
+        <param argument="--mapping_subsampling" type="boolean" truevalue="--mapping_subsampling" falsevalue="" label="Subsampling on the mapping results" help="instead of on the reads"/>
+        <param argument="--subsampling_seed" type="integer" optional="true" label="Subsampling seed" help="No value: random"/>
+    </xml>
 </macros>
diff -r 254cb00a578f -r a755466eb47c test-data/SRS014464-Anterior_nares.fastq.gz
Binary file test-data/SRS014464-Anterior_nares.fastq.gz has changed
diff -r 254cb00a578f -r a755466eb47c test-data/test_database_versioned.loc
--- a/test-data/test_database_versioned.loc	Tue Apr 30 09:08:54 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# 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 254cb00a578f -r a755466eb47c test-data/test_database_versioned.loc.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database_versioned.loc.test	Mon Jul 29 07:14:38 2024 +0000
@@ -0,0 +1,11 @@
+# Tab separated with 5 columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - dbkey
+# - 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
+# the TOY DB should be called in tests with the hidden test parameter enables this will make Metaphlan
+# download the data to the JWD
+mpa_vJan21_TOY_CHOCOPhlAnSGB	mpa_vJan21_TOY_CHOCOPhlAnSGB	mpa_vJan21_TOY_CHOCOPhlAnSGB_202103	./	SGB
+# mpa_vJun23_CHOCOPhlAnSGB_202403	mpa_vJun23_CHOCOPhlAnSGB_202403	mpa_vJun23_CHOCOPhlAnSGB_202403	${__HERE__}/mpa_vJun23_CHOCOPhlAnSGB_202403/	SGB
diff -r 254cb00a578f -r a755466eb47c tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Tue Apr 30 09:08:54 2024 +0000
+++ b/tool_data_table_conf.xml.test	Mon Jul 29 07:14:38 2024 +0000
@@ -2,6 +2,6 @@
 <tables>
     <table name="metaphlan_database_versioned" comment_char="#">
         <columns>value, name, dbkey, path, db_version</columns>
-        <file path="${__HERE__}/test-data/test_database_versioned.loc"/>
+        <file path="${__HERE__}/test-data/test_database_versioned.loc.test"/>
     </table>
 </tables>