# HG changeset patch
# User richard-burhans
# Date 1715017490 0
# Node ID 6c95c380bfa779d5dd82f5fdd3128c6935870834
# Parent  75e15ba3b4c102449a19d78128da225da324da4a
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a4be517dbe8277bed184b915721964820d7a3af0

diff -r 75e15ba3b4c1 -r 6c95c380bfa7 macros.xml
--- a/macros.xml	Wed Apr 24 20:50:20 2024 +0000
+++ b/macros.xml	Mon May 06 17:44:50 2024 +0000
@@ -3,11 +3,11 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">segalign-full</requirement>
             <requirement type="package" version="0.18">bashlex</requirement>
-            <yield/>
+            <requirement type="package" version="3.12">python</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.1.2.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.1.2.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="edam_ontology">
         <edam_operations>
diff -r 75e15ba3b4c1 -r 6c95c380bfa7 segalign.xml
--- a/segalign.xml	Wed Apr 24 20:50:20 2024 +0000
+++ b/segalign.xml	Mon May 06 17:44:50 2024 +0000
@@ -174,8 +174,8 @@
                 <option value="segalign_repeat_masker">SegAlign repeat masker</option>
             </param>
             <when value="segalign">
-                <param name="target" type="data" format="fasta" label="Target sequence file in FASTA format"/>
-                <param name="query" type="data" format="fasta" label="Query sequence file in FASTA format"/>
+                <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/>
+                <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/>
                 <expand macro="sequence_options"/>
                 <expand macro="scoring_options"/>
                 <expand macro="seeding_options"/>
@@ -191,7 +191,7 @@
                 </section>
             </when>
             <when value="segalign_repeat_masker">
-                <param name="seq_file" type="data" format="fasta" label="Sequence file in FASTA format"/>
+                <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/>
                 <expand macro="sequence_options">
                     <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/>
                 </expand>
@@ -224,19 +224,19 @@
     <tests>
         <test expect_num_outputs="1" expect_test_failure="true">
             <param name="mode_selector" value="segalign"/>
-            <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/>
-            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta"/>
+            <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
+            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/>
             <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/>
         </test>
         <test expect_num_outputs="1" expect_test_failure="true">
             <param name="mode_selector" value="segalign_repeat_masker"/>
-            <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/>
+            <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
             <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1" expect_test_failure="true">
             <param name="mode_selector" value="segalign"/>
-            <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/>
-            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta"/>
+            <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
+            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/>
             <param name="diagonal_partition" value="true"/>
             <output name="segalign_diagonal_partition_output" ftype="tgz">
                 <assert_contents>