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annotate seqtk_sample.xml @ 5:a09586d5149a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
author iuc
date Fri, 11 Jan 2019 05:15:20 -0500
parents ecf1c30da3a2
children 288f7f69fe25
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_sample" name="seqtk_sample" version="@TOOL_VERSION@.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[
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10 seqtk sample
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11 -s $s
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12 '$in_file'
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13 $subsample_size
4
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14 @CONDITIONAL_GZIP_OUT@
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15 ]]></command>
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16 <inputs>
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17 <expand macro="in_faq" />
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18 <param argument="-s" type="integer" value="4" label="RNG seed" help="The seed used for the random number generator. Manually specifying a number here is useful for reproducing the same subsampling over time" />
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19 <param name="subsample_size" type="float" value="100" label="Subsample (decimal fraction or number)" />
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20 </inputs>
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21 <outputs>
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22 <data name="default" format_source="in_file" label="Subsample of reads from $in_file.name"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="in_file" value="seqtk_sample.fa"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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27 <param name="subsample_size" value="4"/>
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28 <param name="s" value="4"/>
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29 <output name="default" file="seqtk_sample.out" ftype="fasta"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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30 </test>
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31 <test>
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32 <param name="in_file" value="seqtk_sample.fa.gz" ftype="fasta.gz"/>
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33 <param name="subsample_size" value="4"/>
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34 <param name="s" value="4"/>
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35 <output name="default" file="seqtk_sample.out.gz" ftype="fasta.gz"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 **What it does**
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40
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41 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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43 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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44
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45 @ATTRIBUTION@
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46 ]]></help>
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47 <expand macro="citation" />
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48 </tool>