Mercurial > repos > petr-novak > re_utils
comparison sampleFasta.xml @ 3:e320ef2d105a draft
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| author | petr-novak |
|---|---|
| date | Thu, 05 Sep 2019 09:04:56 -0400 |
| parents | |
| children | c2c69c6090f0 |
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| 2:ff658cf87f16 | 3:e320ef2d105a |
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| 1 <tool id="sampler" name="Sequence sampling" version="1.0.0"> | |
| 2 <description> Tool for creating samples of sequences from larger dataset</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">seqkit</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Error" /> | |
| 8 </stdio> | |
| 9 <command> | |
| 10 #if str($paired)=="true" | |
| 11 ${__tool_directory__}/deinterlacer.py $input Afile Bfile | |
| 12 && | |
| 13 seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile | |
| 14 && | |
| 15 seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile | |
| 16 && | |
| 17 ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile | |
| 18 #else | |
| 19 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input | |
| 20 #end if | |
| 21 </command> | |
| 22 | |
| 23 <inputs> | |
| 24 <param format="fasta" type="data" name="input" label="Choose your fasta file" /> | |
| 25 <param name="number" type="integer" size="7" value="500000" min="1" label="number of sequences or sequence pairs"/> | |
| 26 <param name="seed" type="integer" size="10" value="10" min="0" label="random number generator seed " /> | |
| 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"/> | |
| 28 | |
| 29 | |
| 30 </inputs> | |
| 31 | |
| 32 | |
| 33 <outputs> | |
| 34 <data format="fasta" name="output" label="Random selection from dataset ${input.hid}, sample size ${number})" /> | |
| 35 </outputs> | |
| 36 | |
| 37 <help> | |
| 38 **What it does** | |
| 39 | |
| 40 This tools is intended to create sample of sequences from by taking 'random' sample from larger data sets. | |
| 41 Using a same seed parameter make sampling reproducible. | |
| 42 | |
| 43 | |
| 44 </help> | |
| 45 | |
| 46 | |
| 47 </tool> |