Merge pull request #5275 from tuncK/humann37

Update humann 3.6.1 -> 3.7
galaxyproject · Apr 24, 2023 · 0a3abec · 0a3abec
2 parents 2d2c72d + 4b28ccb
commit 0a3abec
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/tools/humann/humann.xml b/tools/humann/humann.xml
@@ -12,7 +12,8 @@
                     <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" />
+                                <filter type="regexp" column="0" value=".*(vOct22_SGB|TOY|demo-db).*"/>
+                                <validator message="No MetaPhlAn database is available" type="no_options"/>
                             </options>
                         </param>
                     </when>
@@ -56,7 +57,7 @@
         <xml name="nucleotide_search">
             <section name="nucleotide_search" title="Nucleotide search / Mapping reads to community pangenomes"  expanded="true">
                 <conditional name="nucleotide_db">
-                    <param name="selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
+                    <param name="selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN databases">
                         <option value="cached" selected="true">Locally cached</option>
                         <option value="history">From history</option>
                     </param>
@@ -102,7 +103,7 @@
         <xml name="translated_search">
             <section name="translated_search" title="Translated search / Aligning unmapped reads to a protein database" expanded="true">
                 <conditional name="protein_db">
-                    <param name="selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
+                    <param name="selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN databases">
                         <option value="cached" selected="true">Locally cached</option>
                         <option value="history">From history</option>
                     </param>

diff --git a/tools/humann/macros.xml b/tools/humann/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">3.6.1</token>
+    <token name="@TOOL_VERSION@">3.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">

diff --git a/tools/humann/tool-data/metaphlan_database.loc.sample b/tools/humann/tool-data/metaphlan_database.loc.sample
@@ -5,4 +5,4 @@
 # - db-name
 # - build
 # - /path/to/data 
-#02_16_2014	 MetaPhlAn2 clade-specific marker genes	db_v20	/path/to/data
+#02_16_2014	 MetaPhlAn clade-specific marker genes	db_v20	/path/to/data