annotate profrep_masking.xml @ 0:a5f1638b73be draft

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author petr-novak
date Wed, 26 Jun 2019 08:01:42 -0400
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1 <tool id="profrep_mask" name="ProfRep Masker" version="1.0.0">
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2 <description> Tool to mask repetitive regions of original DNA seq based on the repeat regions reported by ProfRep </description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">profrep</requirement>
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5 </requirements>
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6 <command>
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7 python3 ${__tool_directory__}/profrep_masking.py --query ${input} --repeat_gff ${rp_gff} --mode ${mode} --output_masked ${out_masked}
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8 </command>
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9 <inputs>
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10 <param format="fasta" type="data" name="input" label="Choose your input sequence to be masked" help="" />
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11 <param format="gff" type="data" name="rp_gff" label="Choose GFF file of repetitive regions" help="" />
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12 <param name="mode" type="select" label="Select the mode of masking" help="" >
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13 <option value="lowercase" selected="True">lowercase</option>
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14 <option value="N">N</option>/>
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15 </param>
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16
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17 </inputs>
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18
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19 <outputs>
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20 <data format="fasta" name="out_masked" label="Masked DNA sequence(s) from dataset ${input.hid}" />
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21 </outputs>
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22
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23 <help>
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24 **WHAT IT DOES**
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25 This tool will mask repetitive regions of the original DNA sequence(s) based on repeats GFF. You can choose either lowercase(sequence will be preserved) or "N" mode of masking.
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26 </help>
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27 </tool>