Mercurial > repos > p.lucas > taxid_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb
changeset 1:f83dad3524f9 draft
Uploaded xml file v1
| author | p.lucas |
|---|---|
| date | Thu, 21 Sep 2023 15:23:24 +0000 |
| parents | e5b355a33841 |
| children | ad27c2b4e2c3 |
| files | TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.xml |
| diffstat | 1 files changed, 31 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.xml Thu Sep 21 15:23:24 2023 +0000 @@ -0,0 +1,31 @@ +<tool id="TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb" name="Used after Get acc number for complete genome after MEGABLAST_TAB_select_acc_under_taxids" version="1.0"> + <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="8.4.0">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" 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" 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>