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1 <tool id="parse_qualimap" name="Parse Qualimap reports" version="0.1.0">
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2 <description>and output a list of outliers</description>
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3 <command><![CDATA[
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4 $__tool_directory__/qualimap_parser -n #for $report in $reports# ${report.element_identifier} #end for#
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5 -i #for $report in $reports# $report #end for#
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6 ]]></command>
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7 <inputs>
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8 <param name="reports" type="data" format="txt" label="Qualimap Genome Report" help="" optional="false" multiple="True" />
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9 </inputs>
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10 <outputs>
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11 <data name="output_file" label="Outliers from dataset after mapping" format="txt" from_work_dir="outlier_list.txt"/>
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12 </outputs>
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13
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14 <tests>
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15 <test>
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16
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17 </test>
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18 </tests>
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19
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20 <help><![CDATA[
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21 Parses Qualimap reports and outputs a list of outliers based on percentage of the reference genome covered and mean mapping quality.
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22
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23 Command line:
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24 qualimap_parser -n <accessions> -i <reports>
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25
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26 ]]></help>
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27
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28 <citations>
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29 Manuscript in preparation
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30 </citations>
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31 </tool>
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