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

Not_yet_tested_properly
author triasteran
date Tue, 22 Feb 2022 15:38:38 +0000
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-1:000000000000 0:012dc1867dc7
1 <tool id="bam2bigwig" name="Convert Bam to BigWig" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package" version="0.18.0">pysam</requirement>
4 <requirement type="package" version="2.30.0">bedtools</requirement>
5 <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 bam_to_bigwig_py3.py '$input1' --outfile=$output1
9 ]]></command>
10 <inputs>
11 <param type="data" name="input1" format="bam" />
12 </inputs>
13 <outputs>
14 <data name="output1" format="bigwig" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="input1" value="file.bam"/>
19 <output name="output1" file="out.bigwig"/>
20 </test>
21 </tests>
22 <help>
23 <![CDATA[
24 Convert BAM files to BigWig file format in a specified region.
25
26 Usage:
27 bam_to_wiggle.py <BAM file> <YAML config> --outfile=<output file name> ]]>
28 </help>
29 <citations>
30 <citation type="bibtex">
31 @misc{githubbam_to_bigwig,
32 author = {Audrey},
33 year = {2022},
34 title = {bam_to_bigwig},
35 publisher = {GitHub},
36 journal = {GitHub repository},
37 url = {https://github.com/triasteran/RiboGalaxy_tools}, }
38 </citation>
39 </citations>
40 </tool>