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1 <tool id="bam2bigwig" name="Convert Bam to BigWig" version="0.1.1a" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="0.18.0">pysam</requirement>
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4 <requirement type="package" version="2.30.0">bedtools</requirement>
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5 <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python3 '$__tool_directory__/bam_to_bigwig_py3.py' '$input1' --outfile=$output1
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="input1" format="bam" />
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12 </inputs>
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13 <outputs>
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14 <data name="output1" format="bigwig" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input1" value="file.bam"/>
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19 <output name="output1" file="out.bigwig"/>
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20 </test>
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21 </tests>
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22 <help>
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23 <![CDATA[
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24 Convert BAM files to BigWig file format in a specified region.
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25
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26 Usage:
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27 bam_to_wiggle.py <BAM file> <YAML config> --outfile=<output file name> ]]>
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28 </help>
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29 <citations>
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30 <citation type="bibtex">
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31 @misc{githubbam_to_bigwig,
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32 author = {Audrey},
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33 year = {2022},
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34 title = {bam_to_bigwig},
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35 publisher = {GitHub},
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36 journal = {GitHub repository},
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37 url = {https://github.com/triasteran/RiboGalaxy_tools}, }
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38 </citation>
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39 </citations>
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40 </tool>
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