diff bam_to_bigwig.xml @ 7:77114c36b8ab draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig.xml	Mon Aug 29 07:28:10 2016 -0400
@@ -0,0 +1,58 @@
+<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.2.0">
+
+  <description>Calculates coverage from a BAM alignment file</description>
+
+  <requirements>
+    <requirement type="package" version="0.8.3">pysam</requirement>
+    <requirement type="package" version="2.24">bedtools</requirement>
+    <requirement type="package" version="312">ucsc_tools</requirement>
+  </requirements>
+
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[
+    bam_to_bigwig.py $align --outfile=$out --split
+  ]]></command>
+
+  <inputs>
+    <param format="bam" name="align" type="data" label="BAM alignment file"/>
+  </inputs>
+
+  <outputs>
+    <data format="bigwig" name="out" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="align" value="bam_to_bigwig_test.bam"/>
+      <output name="out" file="bam_to_bigwig_test.bigwig"/>
+    </test>
+  </tests>
+
+<help><![CDATA[
+**What it does**
+
+Creates a coverage file in BigWig format, given a BAM alignment file.
+
+Gaps or skips (CIGAR D or N operators) are not counted towards the coverage
+calculation, which is important when mapping RNA Seq reads to genes with
+introns.
+
+**Input**
+
+A BAM alignment file. This needs to have the genome database build used in
+alignment annotated. If your file has '?' for the database build, click on the
+pencil icon to edit the alignment attributes, and specify the organism used to
+align against.
+
+**Output**
+
+BigWig files can be loaded directly from Galaxy into the UCSC browser. They can
+be loaded incrementally by UCSC, so a single file can be used to represent the
+entire genome without having to upload the entire thing as a custom track.
+
+]]></help>
+
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    <citation type="doi">10.1093/bioinformatics/btq033</citation>
+  </citations>
+</tool>