diff macros.xml @ 0:1b08e39cc52d draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit 8f0b5d30f8f5daea0f6c03293c8593ac24d9e1b7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jun 28 08:39:38 2023 +0000
@@ -0,0 +1,31 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.3.1</token>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1101/2023.02.06.527280</citation>
+            <citation type="doi">10.1093/bioinformatics/btaa1044</citation>
+        </citations>
+    </xml>
+
+    <xml name="requirements">
+        <container type="docker">gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.2.0-cudnn8</container>
+    </xml>
+
+    <xml name="subseq" tokens="length,offset,offsetlen">
+        <param argument="--subsequence-length" type="integer" min="0" max="213840" value="@LENGTH@" label="Subsequence length: how much of the genome the Neural Network can see at once" help="Should ideally be comfortably longer than the typical gene. For genomes with large genes (>20kpb) it is recommended to increase this parameter."></param>
+        <conditional name="option_overlap">
+            <param name="use_overlap" type="select" label="Enable overlapping step after predictions" help="This step combines predictions made on each subsequences, to improve quality near start and end of subsequences">
+                <option value="true" selected="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param argument="--overlap-offset" type="integer" min="0" value="@OFFSET@" label="Overlap offset" help="Smaller values may lead to better predictions but will take longer. The subsequence length should be evenly divisible by this value."/>
+                <param argument="--overlap-core-length" type="integer" min="0" value="@OFFSETLEN@" label="Overlap core length" help="Predicted subsequences will be cut to this length to increase prediction quality. Smaller values may lead to better predictions but will take longer. Has to be smaller than subsequence_length."/>
+            </when>
+            <when value="false"/>
+        </conditional>
+    </xml>
+
+</macros>
+