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author stephenshank
date Wed, 28 Jun 2023 16:22:28 +0000
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1 <tool id="regal" name="Read-based evaluation of Genome Assemblies" version="1.0" profile="21.05">
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2 <description>Assembly statistics from a BED coverage file</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1">assemblyqc</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 regal -c $bed -a $ref -o $json -p $percentiles
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8 ]]>
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9 </command>
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10 <inputs>
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11 <param argument="bed" type="data" format="bed" label="BED file" help="BED file containing coverage."/>
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12 <param argument="ref" type="data" format="fasta" label="FASTA file" help="FASTA file of existing assembly."/>
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13 <param argument="percentiles" type="text" label="Percentiles" help="Percentiles for assembly statistics (comma delimited)."/>
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14 </inputs>
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15 <outputs>
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16 <data name="json" format="json" label="${tool.name} on ${on_string}: Assembly JSON"></data>
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17 </outputs>
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18 <tests>
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19 </tests>
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20 <help><![CDATA[
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21
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22 .. class:: infomark
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23
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24 **Purpose**
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25
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26 Calculate some statistics associated to assembly quality.
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27
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28 ------
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29
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30 .. class:: infomark
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31
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32 **Outputs**
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33
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34 This tool generates a JSON file containing contiguous regions and assembly statistics based on the
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35 reads that were used to produce a given assembly.
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36 ]]>
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37 </help>
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38 <citations>
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39 </citations>
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40 </tool>
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