Mercurial > repos > triasteran > bam_to_bigwig
comparison BamToBigWig_planemo/bam2bigwig.xml @ 10:03546efc0470 draft default tip
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| author | triasteran |
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| date | Tue, 22 Feb 2022 16:37:09 +0000 |
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| 9:3961bd62b9d6 | 10:03546efc0470 |
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| 1 <tool id="bam2bigwig" name="Convert Bam to BigWig" version="0.1.1a" 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 python3 '$__tool_directory__/bam_to_bigwig_py3.py' '$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> |