--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/funannotate_sort.xml	Thu Aug 26 06:56:18 2021 +0000
@@ -0,0 +1,63 @@
+<tool id="funannotate_sort" name="Sort assembly" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements" />
+    </requirements>
+    <version_command>funannotate check --show-versions</version_command>
+    <command><![CDATA[
+funannotate sort
+--input '${input}'
+--out '${output}'
+--base '${base}'
+--minlen ${minlen}
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="fasta" label="Assembly to sort" />
+
+        <param argument="--base" type="text" value="scaffold" label="Base name to relabel contigs">
+            <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
+        </param>
+        <param argument="--minlen" type="integer" value="0" label="Shorter contigs are discarded" />
+    </inputs>
+    <outputs>
+        <data name='output' format='fasta' label="${tool.name} on ${on_string}: sorted assembly" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="genome.fa" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text=">scaffold_1" />
+                    <has_text text=">scaffold_4" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="genome.fa" />
+            <param name="base" value="something" />
+            <param name="minlen" value="2100" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text=">something_1" />
+                    <not_has_text text=">something_4" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Funannotate_ sort
+-----------------
+
+Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
+
+This script sorts the input contigs by size (longest->shortest) and then relabels
+the contigs with a simple name (e.g. scaffold_1).  Augustus can have problems with
+some complicated contig names.
+
+.. _Funannotate: http://funannotate.readthedocs.io
+    ]]></help>
+    <expand macro="citations" />
+</tool>