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1 <tool id="parse_refseq_masher" name="Parse refseq_masher matches collection" version="0.1.0">
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2 <description>and output a list of outliers</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.1">ete3</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 $__tool_directory__/refseq_parser $db $taxid #for $report in $reports# $report #end for#
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8 ]]></command>
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9 <inputs>
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10 <param name="db" type="data" format="sqlite" label="(ETE3) Taxonomy Database"/>
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11 <param name="reports" type="data" format="tabular" label="Refseq_masher report" help="" optional="false" multiple="True" />
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12 <param name="taxid" type="integer" value="0" label="Taxonomic ID of target taxonomic rank" optional="false"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output_file" label="Outliers from dataset" format="txt" from_work_dir="outlier_list.txt"/>
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16 </outputs>
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17
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18 <tests>
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19 <test>
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20 <param name="report" value="test.tsv" ftype="tabular" />
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21 <output name="output" value="output.tsv" ftype="tabular" />
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22 </test>
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23 </tests>
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24
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25 <help><![CDATA[
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26 Parses refseq_masher output and returns a list of outliers based on two criteria:
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27
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28 1. If the mash match is not the same or a descendant of the target taxonomic ID
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29 2. If the distance between the match and the sample is >0.05
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30
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31 Command line:
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32 refseq_parser <ETE3 taxonomy database> <taxid> [input refseq_masher reports ...]
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33 ]]></help>
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34
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35 <citations>
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36 Manuscript in preparation
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37 </citations>
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38 </tool>
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