<tool id="TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb" name="Used after Get acc number for complete genome after MEGABLAST_TAB_select_acc_under_taxids" version="1.2">
  <description>
    From a file of taxid and accession numbers (tsv), deduce species taxids, get ref genome acc nr list (all chr).
    (it will allow to have complete genomes when aligning with host to remove host reads)
    provide 2 files:
      - file with all acc numbers that are included in taxid(s) provided by user (extended to genus level)
      - file with all acc numbers that are excluded in taxid(s) provided by user (extended to genus level)
  </description>
  <requirements>
    <requirement type="package" version="3.9.16">python</requirement>
    <requirement type="package" version="3.1.2">ete3</requirement>
    <requirement type="package" version="8.2.0">natsort</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.py' -i ${input} -d ${taxid_host_db} -o ${output}
  ]]></command>
  <inputs>
    <param name="input" format="tsv,txt" type="data" label="Select tsv file with list of taxid and accession number." help="tsv output of MEGABLAST_TAB_select_acc_under_taxids.py (One taxid acc nbr per line)"/>
    <param name="taxid_host_db" format="tsv,txt" type="data" label="Select tsv file for HOSTS." help="taxid acc_number list in tsv (tabular separated at each line) for HOSTS"/>
  </inputs> 
  <outputs>
    <data name="output" format="txt" label="COMPLETE GENOME FROM ${tool.name} on ${on_string}"/>
  </outputs>
  <help>
    From a file of taxid and accession numbers (tsv), deduce species taxids, get ref genome acc nr list (all chr).
    (it will allow to have complete genomes when aligning with host to remove host reads)
    provide 2 files:
      - file with all acc numbers that are included in taxid(s) provided by user (extended to genus level)
      - file with all acc numbers that are excluded in taxid(s) provided by user (extended to genus level)
  </help>
</tool>