annotate sampleFasta.xml @ 7:89c5ba120b21 draft

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author petr-novak
date Mon, 02 Dec 2019 08:41:43 -0500
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1 <tool id="sampler" name="Sequence sampling" version="1.0.0">
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2 <description> Tool for creating samples of sequences from larger dataset</description>
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3 <requirements>
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4 <requirement type="package">seqkit</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error" />
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8 </stdio>
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9 <command>
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10 #if str($paired)=="true"
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11 ${__tool_directory__}/deinterlacer.py $input Afile Bfile
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12 &amp;&amp;
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13 seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile
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14 &amp;&amp;
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15 seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile
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16 &amp;&amp;
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17 ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile
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18 #else
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19 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input
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20 #end if
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21 </command>
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22
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23 <inputs>
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24 <param format="fasta" type="data" name="input" label="Choose your fasta file" />
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25 <param name="number" type="integer" size="7" value="500000" min="1" label="number of sequences or sequence pairs"/>
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26 <param name="seed" type="integer" size="10" value="10" min="0" label="random number generator seed " />
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27 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="All sequence reads are paired" help="check if you are using pair reads and and input sequences contain both read mates and left mates alternate with their right mates"/>
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29
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30 </inputs>
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33 <outputs>
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34 <data format="fasta" name="output" label="Random selection from dataset ${input.hid}, sample size ${number})" />
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35 </outputs>
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36
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37 <help>
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38 **What it does**
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39
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40 This tools is intended to create sample of sequences from by taking 'random' sample from larger data sets.
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41 Using a same seed parameter make sampling reproducible.
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42
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43
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44 </help>
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45
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46
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47 </tool>