changeset 0:3799012ce2ff draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph commit b3c2bbc3342107c35a1dee05ccc1e4eddffd8a50-dirty
author bgruening
date Tue, 22 Sep 2015 04:12:40 -0400
parents
children
files bigwig_to_bedgraph.xml test-data/bigWigToBedGraph.bw test-data/bigWigToBedGraph_result1.bedgraph test-data/bigWigToBedGraph_result2.bedgraph test-data/bigWigToBedGraph_test2.bw tool_dependencies.xml
diffstat 6 files changed, 58 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwig_to_bedgraph.xml	Tue Sep 22 04:12:40 2015 -0400
@@ -0,0 +1,37 @@
+<tool id="bigwig_to_bedgraph" name="bigWigToBedGraph" version="0.1.0">
+    <description>
+        Convert from bigWig to bedGraph format
+    </description>
+    <requirements>
+        <requirement type="package" version="312">ucsc_tools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        bigWigToBedGraph "${input}" "${output}"
+    ]]></command>
+    <inputs>
+        <param format="bigwig" name="input" type="data" label="bigwig file to convert" help=""/>
+    </inputs>
+    <outputs>
+        <data format="bedgraph" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="bigWigToBedGraph.bw" ftype="bigwig"/>
+            <output name="output" file="bigWigToBedGraph_result1.bedgraph" ftype="bedgraph" />
+        </test>
+        <test><!-- The following crashes on old binaries of bigWigToBedGraph -->
+            <param name="input" value="bigWigToBedGraph_test2.bw" ftype="bigwig"/>
+            <output name="output" file="bigWigToBedGraph_result2.bedgraph" ftype="bedgraph" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Converts bigWig files to bedGraph format.
+
+    ]]></help>
+</tool>
Binary file test-data/bigWigToBedGraph.bw has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigWigToBedGraph_result1.bedgraph	Tue Sep 22 04:12:40 2015 -0400
@@ -0,0 +1,11 @@
+chrM	0	210	47
+chrM	210	220	46
+chrM	220	230	41
+chrM	230	240	32
+chrM	240	250	24
+chrM	250	260	13
+chrM	260	16310	10
+chrM	16310	16320	9
+chrM	16320	16330	5
+chrM	16330	16340	4
+chrM	16340	16350	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigWigToBedGraph_result2.bedgraph	Tue Sep 22 04:12:40 2015 -0400
@@ -0,0 +1,4 @@
+chr1	210	220	46
+chr2	210	220	46
+chr3	0	210	47
+gacvbdefgrthjinhgacvbdefgrthjinhgacvefgrthjinhga	210	220	46
Binary file test-data/bigWigToBedGraph_test2.bw has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 22 04:12:40 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ucsc_tools" version="312">
+        <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>