Mercurial > repos > galaxyp > eggnog_mapper

diff eggnog_mapper_annotate.xml @ 15:02439eb2b37d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
author galaxyp
date Mon, 19 Jan 2026 22:22:55 +0000
parents 844fa988236b
children
line wrap: on
line diff
--- 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