view profrep_masking.xml @ 0:a5f1638b73be draft

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<tool id="profrep_mask" name="ProfRep Masker" version="1.0.0">
<description> Tool to mask repetitive regions of original DNA seq based on the repeat regions reported by ProfRep </description>
<requirements>
    <requirement type="package" version="1.0.0">profrep</requirement>
</requirements>
<command>
python3 ${__tool_directory__}/profrep_masking.py --query ${input} --repeat_gff ${rp_gff} --mode ${mode} --output_masked ${out_masked}
</command>
<inputs>
 <param format="fasta" type="data" name="input" label="Choose your input sequence to be masked" help="" />
 <param format="gff" type="data" name="rp_gff" label="Choose GFF file of repetitive regions" help="" />
 <param name="mode" type="select" label="Select the mode of masking" help="" >
	 <option value="lowercase" selected="True">lowercase</option>
     <option value="N">N</option>/>
 </param>

</inputs>

<outputs>
 <data format="fasta" name="out_masked" label="Masked DNA sequence(s) from dataset ${input.hid}" />
</outputs>

<help>
**WHAT IT DOES**
 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.
</help>
</tool>