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author stephenshank
date Wed, 28 Jun 2023 16:22:28 +0000
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1 <tool id="bamtocov" name="BAM to Coverage" version="1.0" profile="21.05">
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2 <description>Get a BED file of coverage from a BAM</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.0">bamtocov</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 bamtocov '$bam' > '$bed'
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8 ]]>
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9 </command>
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10 <inputs>
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11 <param argument="bam" type="data" format="bam" label="BAM file" help="BAM file to get coverage from."/>
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12 </inputs>
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13 <outputs>
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14 <data name="bed" format="bed" label="${tool.name} on ${on_string}: Coverage"></data>
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15 </outputs>
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16 <tests>
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17 </tests>
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18 <help><![CDATA[
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19
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20 .. class:: infomark
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21
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22 **Purpose**
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23
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24 Calculate coverage from a BAM file.
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25
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26 ------
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27
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28 .. class:: infomark
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29
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30 **Outputs**
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31
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32 This tool generates a BED file containing coverage information from the associated BAM file.
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33 ]]>
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34 </help>
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35 <citations>
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36 <citation type="bibtex">
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37 @article{birolo2022bamtocov,
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38 title={BamToCov: an efficient toolkit for sequence coverage calculations},
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39 author={Birolo, Giovanni and Telatin, Andrea},
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40 journal={Bioinformatics},
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41 volume={38},
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42 number={9},
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43 pages={2617--2618},
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44 year={2022},
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45 publisher={Oxford University Press}
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46 }
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47 </citation>
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48 </citations>
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49 </tool>