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1 <?xml version="1.0"?>
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2 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
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1
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3 <description>random subsample of fasta or fastq sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk sample -s $s
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10 $in_file
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11 $subsample_size
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12 > $default]]></command>
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13 <inputs>
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14 <expand macro="in_faq" />
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15 <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
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16 <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/>
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17 </inputs>
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18 <outputs>
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19 <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="in_file" value="seqtk_sample.fa"/>
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24 <param name="subsample_size" value="4"/>
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25 <param name="s" value="4"/>
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26 <output name="default" file="seqtk_sample.out" ftype="fasta"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31
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32 Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
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33
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34 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
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35
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36 @ATTRIBUTION@
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37 ]]></help>
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38 </tool>
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