Mercurial > repos > iuc > crossmap_bam

changeset 7:e5340c09200a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:18:13 +0000
parents 60ca8d013263
children e13f565068d6
files crossmap_bam.xml macros.xml test-data/test_bam_01_output_a.bam test-data/test_bed_02_output_a__all.bed test-data/test_bed_02_output_a__only_fails.bed test-data/test_bigwig_01_output_a.bw test-data/test_region.bed
diffstat 7 files changed, 17 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_bam.xml	Wed Sep 30 14:00:15 2020 +0000
+++ b/crossmap_bam.xml	Thu Jul 15 16:18:13 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@">
+<tool id="crossmap_bam" name="CrossMap BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -46,7 +46,7 @@
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="False"/>
 
-            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
             <param name="index_source" value="cached"/>
@@ -54,7 +54,7 @@
             <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
             <param name="include_fails" value="False"/>
 
-            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Wed Sep 30 14:00:15 2020 +0000
+++ b/macros.xml	Thu Jul 15 16:18:13 2021 +0000
@@ -6,8 +6,8 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.3.7</token>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
+    <token name="@TOOL_VERSION@">0.5.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
Binary file test-data/test_bam_01_output_a.bam has changed
--- a/test-data/test_bed_02_output_a__all.bed	Wed Sep 30 14:00:15 2020 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jul 15 16:18:13 2021 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000	Fail
-chr2	100	10000	Fail
-chr3	100	10000	Fail
-chr4	8941700 8947200	Fail
-chr5	1	100000000	Fail
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
--- a/test-data/test_bed_02_output_a__only_fails.bed	Wed Sep 30 14:00:15 2020 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jul 15 16:18:13 2021 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000
-chr2	100	10000
-chr3	100	10000
-chr4	8941700 8947200
-chr5	1	100000000
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
Binary file test-data/test_bigwig_01_output_a.bw has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_region.bed	Thu Jul 15 16:18:13 2021 +0000
@@ -0,0 +1,2 @@
+chr2	90000	990000	map_ratio=1.0000
+chr3	75000	975000	map_ratio=1.0000