annotate long2short.xml @ 1:5596bafd2119 draft

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author petr-novak
date Tue, 12 Dec 2017 04:33:04 -0500
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1
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1 <tool id="long2short" name="Get pseudo short paired end reads from long reads" version="0.1.0">
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2 <requirements>
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3 <requirement type="package">biopython</requirement>
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4 <requirement type="package" version="3.6">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python3 $__tool_directory__/long2short.py -i "$input1" -o "$output1" -cov ${coverage} -L ${insert_length} -l ${read_length}
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="fasta" />
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11 <param type="integer" name="insert_length" value="1000" />
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12 <param type="integer" name="read_length" value="300" />
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13 <param type="float" name="coverage" value="0.1" min="0.0001" max="10"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output1" format="fasta" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1" value="read_10k_ALL_oxford_nanopore_sample" />
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21 <param name="cov" value="0.1" />
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22 <param name="insert_length" value="600" />
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23 <param name="read_length" value="100" />
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24 <output name="output1" file="pseudo_paired_end.fasta"/>
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25 </test>
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26 </tests>
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27 <help><![CDATA[ Create pseudo short paired-edn reads from long read with
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28 required read length, insert length and coverage. Original position on long
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29 reads is kept as part of the read name ]]></help>
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30
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31 </tool>