diff data_manager/eggnog_macros.xml @ 3:5a2ffc486246 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"

--- a/data_manager/eggnog_macros.xml	Fri Feb 19 18:53:40 2021 +0000
+++ b/data_manager/eggnog_macros.xml	Tue Jan 25 13:50:50 2022 +0000
@@ -1,14 +1,15 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@VERSION@">2.0.1</token>
-   <token name="@EGGNOG_DB_VERSION@">2.0</token>
+   <token name="@VERSION@">2.1.6</token>
+   <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
     <!--
-    # Versionning is super confusing:
+    # DB versionning was super confusing for eggnog-mapper 2.0.x:
     # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
-    # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
-    # db v4.5 are not compatible with eggnog-mapper 2.0
+    # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
+    # (db v4.5 are not compatible with eggnog-mapper 2.0)
+    # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
     -->
-   <token name="@IDX_VERSION@">2.0</token>
+   <token name="@IDX_VERSION@">5.0.2</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1093/nar/gkv1248</citation>
@@ -26,6 +27,8 @@
     <xml name="data_manager_params">
         <param name="test" type="hidden" value="false" />
         <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>
+        <param name="mmseqs_database" type="boolean" truevalue="-M" falsevalue="" checked="true" label="Install the MMseqs2 database" help="Required for mmseqs seed ortholog search mode. Takes ~11Gb, you most probably want it."/>
+        <param name="pfam_database" type="boolean" truevalue="-P" falsevalue="" checked="true" label="Install the Pfam database" help="Rquired for de novo annotation or realignment. Takes ~3Gb, you most probably want it."/>
     </xml>
     <xml name="data_manager_outputs">
         <outputs>
@@ -40,7 +43,7 @@
 #end if
 mkdir -p '${install_path}' &&
 download_eggnog_data.py
-  $diamond_database -y -q
+  $diamond_database $mmseqs_database $pfam_database -y -q
 #if $test == 'true'
   -s
 #end if