# HG changeset patch
# User galaxyp
# Date 1768861375 0
# Node ID 02439eb2b37d15d66cdca279fb39fcbc1daa76ee
# Parent  d9c3016f7283160d00efe6c23aff0507abfc3e3d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001

diff -r d9c3016f7283 -r 02439eb2b37d eggnog_macros.xml
--- a/eggnog_macros.xml	Thu Sep 07 18:51:23 2023 +0000
+++ b/eggnog_macros.xml	Mon Jan 19 22:22:55 2026 +0000
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@TOOL_VERSION@">2.1.8</token>
-   <token name="@VERSION_SUFFIX@">4</token>
+   <token name="@TOOL_VERSION@">2.1.13</token>
+   <token name="@VERSION_SUFFIX@">0</token>
    <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
-   <token name="@PROFILE@">22.01</token>
+   <token name="@PROFILE@">25.0</token>
     <!--
     # DB versionning was super confusing for eggnog-mapper 2.0.x:
     # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
@@ -23,6 +23,11 @@
             <requirement type="package" version="@TOOL_VERSION@">eggnog-mapper</requirement>
         </requirements>
     </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">eggnog-mapper-v2</xref>
+        </xrefs>
+    </xml>
     <xml name="version_command">
         <version_command>emapper.py --version</version_command>
     </xml>
@@ -527,10 +532,10 @@
             <actions>
                 <conditional name="output_options.md5">
                     <when value="True">
-                        <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
+                        <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,eggNOG_OGs,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
                     </when>
                     <when value="False">
-                        <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
+                        <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,eggNOG_OGs,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
                     </when>
                 </conditional>
             </actions>
@@ -610,7 +615,7 @@
         - ``species``
         - ``orthologs`` comma-separated list of orthologs (If an ortholog shows a "*", such ortholog was used to transfer its annotations to the query.)
         
-        **sequences without annotation **
+        **sequences without annotation**
 
         This output is created if cached annotations are used as input. 
         It is a FASTA file containing all sequences that are not found in the cached annotations.
diff -r d9c3016f7283 -r 02439eb2b37d eggnog_mapper.xml
--- a/eggnog_mapper.xml	Thu Sep 07 18:51:23 2023 +0000
+++ b/eggnog_mapper.xml	Mon Jan 19 22:22:55 2026 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>eggnog_macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
@@ -197,7 +198,6 @@
 @HELP_ANNOTATION_OUTPUTS@
 
 
-
 **Recommentation for large input data**
 
 EggNOG-mapper consists of two phases
diff -r d9c3016f7283 -r 02439eb2b37d eggnog_mapper_annotate.xml
--- a/eggnog_mapper_annotate.xml	Thu Sep 07 18:51:23 2023 +0000
+++ b/eggnog_mapper_annotate.xml	Mon Jan 19 22:22:55 2026 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>eggnog_macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
@@ -40,9 +41,11 @@
         <!-- test producing annotations form seed orthologs -->
         <test expect_num_outputs="1">
             <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
-            <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
-                <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
-            </param>
+            <conditional name="ortho_method">
+                <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
+                    <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
+                </param>
+            </conditional>
             <conditional name="annotation_options">
             </conditional>
             <section name="output_options">
@@ -78,9 +81,11 @@
         <!-- test setting tax scope-->
         <test expect_num_outputs="2">
             <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
-            <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
-                <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
-            </param>
+            <conditional name="ortho_method">
+                <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
+                    <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
+                </param>
+            </conditional>
             <section name="annotation_options">
                 <param name="tax_scope" value="651137" />
             </section>
@@ -138,4 +143,4 @@
 
     ]]></help>
     <expand macro="citations"/>
-</tool>
+</tool>
\ No newline at end of file
diff -r d9c3016f7283 -r 02439eb2b37d eggnog_mapper_search.xml
--- a/eggnog_mapper_search.xml	Thu Sep 07 18:51:23 2023 +0000
+++ b/eggnog_mapper_search.xml	Mon Jan 19 22:22:55 2026 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>eggnog_macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[