# HG changeset patch
# User iuc
# Date 1761327987 0
# Node ID 64d732725a73ee8abe37e6c946b78f48fd3e4f11
# Parent  7e353b95f0b6f64c7b4b1a698d3e25f2e1f9ab47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain commit 420bba1b6a3ac4747a282f4c183fcd985a1a9075

diff -r 7e353b95f0b6 -r 64d732725a73 axtchain.xml
--- a/axtchain.xml	Mon Jun 30 10:32:16 2025 +0000
+++ b/axtchain.xml	Fri Oct 24 17:46:27 2025 +0000
@@ -1,9 +1,10 @@
-<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT">
     <description>
         Chain together axt alignments
     </description>
     <macros>
         <token name="@TOOL_VERSION@">482</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
@@ -27,7 +28,7 @@
         #else
             -linearGap=$linear_gap_options.linear_gap
         #end if
-        '$in_axt'
+        <(gzip -cdfq '$in_axt')
         '$in_target'
         '$in_query'
         '$out'
@@ -66,6 +67,15 @@
             </conditional>
             <output name="out" file="hg38.chrM.mm39.chrM.chain" />
         </test>
+        <test>
+            <param name="in_axt" value="hg38.chrM.mm39.chrM.axt.gz" />
+            <param name="in_target" value="hg38.chrM.fasta" />
+            <param name="in_query" value="mm39.chrM.fasta" />
+            <conditional name="linear_gap_options">
+                <param name="linear_gap" value="medium" />
+            </conditional>
+            <output name="out" file="hg38.chrM.mm39.chrM.chain" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 7e353b95f0b6 -r 64d732725a73 test-data/hg38.chrM.mm39.chrM.axt.gz
Binary file test-data/hg38.chrM.mm39.chrM.axt.gz has changed