diff BamToBigWig_planemo/bam2bigwig.xml @ 0:012dc1867dc7 draft

Not_yet_tested_properly

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BamToBigWig_planemo/bam2bigwig.xml	Tue Feb 22 15:38:38 2022 +0000
@@ -0,0 +1,40 @@
+<tool id="bam2bigwig" name="Convert Bam to BigWig" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="0.18.0">pysam</requirement>
+        <requirement type="package" version="2.30.0">bedtools</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>        
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bam_to_bigwig_py3.py '$input1' --outfile=$output1
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="bam" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="bigwig" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="file.bam"/>
+            <output name="output1" file="out.bigwig"/>
+        </test>
+    </tests>
+    <help>
+      <![CDATA[
+Convert BAM files to BigWig file format in a specified region.
+
+Usage:
+    bam_to_wiggle.py <BAM file> <YAML config> --outfile=<output file name> ]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+           @misc{githubbam_to_bigwig,
+  author = {Audrey},
+  year = {2022},
+  title = {bam_to_bigwig},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/triasteran/RiboGalaxy_tools}, }
+        </citation>
+    </citations>
+</tool>