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1 <tool id="coverage_stats" name="Coverage Statistics">
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2 <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
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1
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3 <requirements>
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4 <requirement type="package">mimodd</requirement>
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5 </requirements>
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6 <version_command>mimodd version -q</version_command>
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7 <command>
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8 mimodd covstats "$ifile" --ofile "$output_vcf"
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9 </command>
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10
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11 <inputs>
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12 <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
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13 </inputs>
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14 <outputs>
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15 <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
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16 </outputs>
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17
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18 <help>
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19 .. class:: infomark
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20
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21 **What it does**
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22
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23 The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
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24
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25 .. class:: warningmark
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26
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27 The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites.
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28
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29 </help>
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30 </tool>
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