# HG changeset patch
# User iuc
# Date 1725278394 0
# Node ID 436fb49ce7ec7494148e95336bdcbad1d0dea2df
# Parent  08209a7c4cb703731f588cc19e45e6822336232c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568

diff -r 08209a7c4cb7 -r 436fb49ce7ec crossmap_region.xml
--- a/crossmap_region.xml	Thu Jan 20 04:26:07 2022 +0000
+++ b/crossmap_region.xml	Mon Sep 02 11:59:54 2024 +0000
@@ -7,7 +7,7 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-CrossMap.py region
+CrossMap region
     '${chain_source.input_chain}'
     '${input}'
     $output
@@ -15,9 +15,8 @@
     --ratio $ratio
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="bed" label="BED file"
-               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
-        <expand macro="chain" />
+        <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
+        <expand macro="chain"/>
         <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
         <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
             <option value="a" selected="true">Default (a)</option>
@@ -78,7 +77,6 @@
 7. If input region cannot be consecutively mapped target assembly, it will be split.
 8. \*.unmap file contains regions that cannot be unambiguously converted.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>
diff -r 08209a7c4cb7 -r 436fb49ce7ec macros.xml
--- a/macros.xml	Thu Jan 20 04:26:07 2022 +0000
+++ b/macros.xml	Mon Sep 02 11:59:54 2024 +0000
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <macros>
     <xml name="requirements">
         <requirements>
@@ -6,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.6.1</token>
+    <token name="@TOOL_VERSION@">0.7.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="stdio">
         <stdio>
@@ -17,7 +16,7 @@
     </xml>
     <xml name="version_command">
         <version_command><![CDATA[
-CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
+CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
         ]]></version_command>
     </xml>
     <xml name="chain">