# HG changeset patch
# User iuc
# Date 1725278485 0
# Node ID 6ee334657360b94ddaf0f515b301fa3a5ee10afa
# Parent  158b5b2a164af5c0f1218dbff768eaf416fa8c61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568

diff -r 158b5b2a164a -r 6ee334657360 crossmap_bam.xml
--- a/crossmap_bam.xml	Thu Jan 20 04:33:19 2022 +0000
+++ b/crossmap_bam.xml	Mon Sep 02 12:01:25 2024 +0000
@@ -10,7 +10,7 @@
 
 ln -s '${input}' ./input.bam &&
 
-CrossMap.py bam
+CrossMap bam
 '${chain_source.input_chain}'
 $optional_tags
 
@@ -23,33 +23,27 @@
     ]]></command>
     <inputs>
         <param name="input" type="data" format="bam" label="BAM file"/>
-
-        <expand macro="chain" />
-
+        <expand macro="chain"/>
         <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
-
         <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
         <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
-        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange"
-            help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
+        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
+        <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam"/>
         <!-- CrossMap 0.2.5 does not produce output_unmapped -->
     </outputs>
-
     <tests>
         <test>
             <param name="index_source" value="history"/>
             <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
         </test>
         <test>
             <param name="index_source" value="cached"/>
             <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
-            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -112,7 +106,6 @@
 SU
     uniquely mapped
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>
diff -r 158b5b2a164a -r 6ee334657360 macros.xml
--- a/macros.xml	Thu Jan 20 04:33:19 2022 +0000
+++ b/macros.xml	Mon Sep 02 12:01:25 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">