changeset 0:dd444ce346ae draft default tip

planemo upload commit 54155cb43a07d563ee6861c2410a167b9c879ff4-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Thu Jul 14 18:55:27 2016 -0400
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+The MIT License (MIT)
+
+Copyright (c) 2016 Rémi Marenco
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Jul 14 18:55:27 2016 -0400
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+# bamToBigwig
+Galaxy wrapper for Bam to Bigwig conversion

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig.xml	Thu Jul 14 18:55:27 2016 -0400
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+<tool id="bam_to_bigwig" name="Convert Bam to BigWig" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="312">ucsc_tools</requirement>
+        <requirement type="package" version="2.24">bedtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        faToTwoBit $input_reference_fasta two_bit.2bit;
+        twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes;
+        bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg;
+        bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
+    ]]></command>
+    <inputs>
+        <param format="bam" name="input_bam" type="data" label="Choose BAM file" />
+        <param format="fasta" name="input_reference_fasta"
+               type="data" label="Choose Reference Genome (Fasta)" />
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="output_bigwig" />
+    </outputs>
+    <help>
+        This tool converts a Bam file to a BigWig file.
+
+        It needs:
+            - A Bam file
+            - The reference genome as a Fasta file
+    </help>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 14 18:55:27 2016 -0400
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+<?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>
+
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+</tool_dependency>