# HG changeset patch
# User iuc
# Date 1725278425 0
# Node ID 8dd8edcd39700d0ae11f5890325aed66b1807e4f
# Parent  1b0de2da29a0c330c90fa243b7ed490eeb8a76df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568

diff -r 1b0de2da29a0 -r 8dd8edcd3970 crossmap_gff.xml
--- a/crossmap_gff.xml	Thu Jan 20 04:28:49 2022 +0000
+++ b/crossmap_gff.xml	Mon Sep 02 12:00:25 2024 +0000
@@ -6,9 +6,8 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
-
     <command><![CDATA[
-CrossMap.py gff
+CrossMap gff
 '${chain_source.input_chain}'
 '${input}'
 
@@ -18,26 +17,20 @@
 
 output
     ]]></command>
-
     <inputs>
         <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
-
-        <expand macro="chain" />
-
+        <expand macro="chain"/>
         <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output" />
+        <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output"/>
     </outputs>
-
     <tests>
         <test>
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="False"/>
-
             <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
         </test>
         <test>
@@ -45,14 +38,13 @@
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="True"/>
-
             <output name="output" file="test_gff_01_output_a__all.gtf"/>
         </test>
-        <test><!-- cached chain file -->
+        <test>
+            <!-- cached chain file -->
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/>
             <param name="index_source" value="cached"/>
             <param name="include_fails" value="True"/>
-
             <output name="output" file="test_gff_01_output_a__all.gtf"/>
         </test>
     </tests>
@@ -75,7 +67,6 @@
   the same gene were converted into the same gene.
 - If user want to liftover gene annotation files, use BED12 format.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>
diff -r 1b0de2da29a0 -r 8dd8edcd3970 macros.xml
--- a/macros.xml	Thu Jan 20 04:28:49 2022 +0000
+++ b/macros.xml	Mon Sep 02 12:00:25 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">