changeset 2:1597f4ccde5d draft

planemo upload for repository https://github.com/vgl-hub/rdeval commit a88c3bbf27ea89ea8bdc7d8b7d2cdfaa7ebd1af8

--- a/macros.xml	Mon Feb 17 19:31:33 2025 +0000
+++ b/macros.xml	Tue Feb 18 16:55:03 2025 +0000
@@ -1,33 +1,26 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">rdeval</requirement>
-        </requirements>
-    </xml>
-    <token name="@TOOL_VERSION@">0.0.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">23.02</token>
-    <token name="@ATTRIBUTION@"><![CDATA[
-        **Attribution**
-        
-        This Galaxy tool is available at `vgl-hub/rdeval <https://github.com/vgl-hub/rdeval/>`_, and
-        relies on the gfastar suite and the gfalibs toolkit `vgl-hub/gfalibs
-        <https://github.com/vgl-hub/gfalibs>`_, developed by Giulio Formenti at the Rockefeller University
-        ]]></token>
-    <xml name="citations">
-        <citations>
-            <citation type="bibtex">
-                @article{formenti2022gfastats,
-                    title={Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs},
-                    author={Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Crist{\'o}bal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D},
-                    journal={Bioinformatics},
-                    volume={38},
-                    number={17},
-                    pages={4214--4216},
-                    year={2022},
-                    publisher={Oxford University Press}
-                    }
-            </citation>
-        </citations>
-    </xml>
-</macros>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">rdeval</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.0.5</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">23.02</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{formenti2022gfastats,
+                    title={Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs},
+                    author={Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Crist{\'o}bal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D},
+                    journal={Bioinformatics},
+                    volume={38},
+                    number={17},
+                    pages={4214--4216},
+                    year={2022},
+                    publisher={Oxford University Press}
+                    }
+            </citation>
+        </citations>
+    </xml>
+</macros>

--- a/rdeval.xml	Mon Feb 17 19:31:33 2025 +0000
+++ b/rdeval.xml	Tue Feb 18 16:55:03 2025 +0000
@@ -32,7 +32,7 @@
 	#if $input_subsample.seed_selector == "yes"
 		--random-seed '$random_seed'
 	#end if
-	#if $homopolymer_compress.compress_selector == "yes"
+	#if $input_compress.compress_selector == "yes"
 		--homopolymer-compress '$homopolymer_compress'
 	#end if
     #if $stats_flavor.flavor_selector == "stats"
@@ -92,7 +92,7 @@
                 </when>
             </conditional>
         </section>
-        <conditional name="homopolymer_compress">
+        <conditional name="input_compress">
             <param name="compress_selector" type="select" label="Compress homopolymers">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
@@ -242,7 +242,9 @@
 	-v --version software version.
 	--cmd print $0 to stdout.
 
-@ATTRIBUTION@
+**Attribution**
+
+This tool relies on the gfastar suite and the gfalibs toolkit `vgl-hub/gfalibs <https://github.com/vgl-hub/gfalibs>`_, developed by Giulio Formenti at the Rockefeller University
     ]]></help>
     <expand macro="citations"/>
 </tool>