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author petr-novak
date Wed, 26 Jun 2019 08:51:23 -0400
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<tool id="extract_data" name="Extract Data For ProfRep" version="1.0.0">
<requirements><requirement type="package" version="1.0.0">profrep</requirement></requirements>
<description> Extract data for ProfRep from RepaetExplorer </description>
<command>
python3 ${__tool_directory__}/extract_data_for_profrep.py --re_archive ${re_archive} --output_cls ${output_cls} --output_reads_all ${output_reads_all} --output_annotation ${output_annotation}
</command>
<inputs>
 <param format="zip" type="data" name="re_archive" label="RepeatExplorer output data archive" help="" />
</inputs>

<outputs>
 <data format="fasta" name="output_cls" label="Output cls file of all clusters from ${re_archive.hid} archive" />
 <data format="fasta" name="output_reads_all" label="Output file of all reads sequences from ${re_archive.hid} archive" />
 <data format="tabular" name="output_annotation" label="Output file of clusters annotation from ${re_archive.hid} archive" />
</outputs>

 <help>

**WHAT IT DOES**

This tool will extract all the necessary input data that are needed for ProfRep from RE output archive.
Use if the species is not already provided in our internal database (ProfRep drop-down menu -> Choose existing annotation dataset)


 </help>
</tool>