# HG changeset patch
# User iuc
# Date 1725278438 0
# Node ID cdb491bbf1d24d2487eb3f233a147b33af10edfc
# Parent  aa85f6cf1d16021901a6f152214443d643c2d736
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568

diff -r aa85f6cf1d16 -r cdb491bbf1d2 crossmap_bed.xml
--- a/crossmap_bed.xml	Thu Jan 20 04:27:28 2022 +0000
+++ b/crossmap_bed.xml	Mon Sep 02 12:00:38 2024 +0000
@@ -6,8 +6,7 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
-
-<!--
+    <!--
 1. CrossMap bed x.chain in.bed > out.bed
 stdout/out.bed: valid and invalid combined
 
@@ -16,7 +15,7 @@
 out.bed.unmap: invalid only
 -->
     <command><![CDATA[
-CrossMap.py bed
+CrossMap bed
 '${chain_source.input_chain}'
 '${input}'
 
@@ -28,13 +27,9 @@
 #end if
 --chromid $chromid
     ]]></command>
-
-
     <inputs>
-        <param name="input" type="data" format="bed" label="BED file"
-               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
-
-        <expand macro="chain" />
+        <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
+        <expand macro="chain"/>
         <param name="chromid" type="select" label="Style of chromosome IDs">
             <option value="a" selected="true">As-is</option>
             <option value="l">Long style, e.g. chr1, chrX</option>
@@ -42,7 +37,6 @@
         </param>
         <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
     </inputs>
-
     <outputs>
         <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
             <filter>merge_unmapped_entries is False</filter>
@@ -50,56 +44,52 @@
         <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
             <filter>merge_unmapped_entries is False</filter>
         </data>
-
         <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
             <filter>merge_unmapped_entries is True</filter>
         </data>
     </outputs>
-
     <tests>
-        <test><!-- this test only contains perfect entries that do get liftOvered (separate output) -->
+        <test expect_num_outputs="2">
+            <!-- this test only contains perfect entries that do get liftOvered (separate output) -->
             <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <param name="merge_unmapped_entries" value="false" />
-
+            <param name="merge_unmapped_entries" value="false"/>
             <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
             <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
         </test>
-        <test><!-- this test only contains perfect entries that do get liftOvered (merged output) -->
+        <test expect_num_outputs="1">
+            <!-- this test only contains perfect entries that do get liftOvered (merged output) -->
             <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="merge_unmapped_entries" value="true" />
-
+            <param name="merge_unmapped_entries" value="true"/>
             <output name="output_combined" file="test_bed_01_output_a__all.bed"/>
         </test>
-
-        <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
+        <test expect_num_outputs="2">
+            <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
             <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="merge_unmapped_entries" value="false" />
-            <param name="chromid" value="s" />
-
+            <param name="merge_unmapped_entries" value="false"/>
+            <param name="chromid" value="s"/>
             <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
             <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
         </test>
-        <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
+        <test expect_num_outputs="1">
+            <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
             <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="merge_unmapped_entries" value="true" />
-            <param name="chromid" value="s" />
-
+            <param name="merge_unmapped_entries" value="true"/>
+            <param name="chromid" value="s"/>
             <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
         </test>
-
-        <test><!-- clone of first test: tests cached reference chain file -->
+        <test expect_num_outputs="2">
+            <!-- clone of first test: tests cached reference chain file -->
             <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/>
             <param name="index_source" value="cached"/>
-            <param name="merge_unmapped_entries" value="false" />
-
+            <param name="merge_unmapped_entries" value="false"/>
             <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
             <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
         </test>
@@ -141,7 +131,6 @@
 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 aa85f6cf1d16 -r cdb491bbf1d2 macros.xml
--- a/macros.xml	Thu Jan 20 04:27:28 2022 +0000
+++ b/macros.xml	Mon Sep 02 12:00:38 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">