Mercurial > repos > p.lucas > taxid_genusexpand_taxid2acc
changeset 1:7f0de5b912b5 draft
Uploaded 09 03 23 first upload of the wrapper
| author | p.lucas |
|---|---|
| date | Thu, 09 Mar 2023 16:51:05 +0000 |
| parents | e7dd595fb0dd |
| children | 830e4f00d55b |
| files | TAXID_genusexpand_taxid2acc.xml |
| diffstat | 1 files changed, 26 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TAXID_genusexpand_taxid2acc.xml Thu Mar 09 16:51:05 2023 +0000 @@ -0,0 +1,26 @@ +<tool id="TAXID_genusexpand_taxid2acc" name="Get acc number for complete genome after MEGABLAST_TAB_select_acc_under_taxids" version="1"> + <description> + From a taxid and acc number file of results (output of MEGABLAST_TAB_select_acc_under_taxids.py) + provide 1 file: + - file with all acc numbers for complete genomes + </description> + <requirements> + <requirement type="package" version="3.9.16">python</requirement> + <requirement type="package" version="3.1.2">ete3</requirement> + <requirement type="package" version="3.0.0">ete_toolchain</requirement> + <requirement type="package" version="0.3.1">ncbi-genome-download</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/TAXID_genusexpand_taxid2acc' -i ${input} -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)"/> + </inputs> + <outputs> + <data name="output" format="txt" label="COMPLETE GENOME FROM ${tool.name} on ${on_string}"/> + </outputs> + <help> +From the tsv output file of MEGABLAST_TAB_select_acc_under_taxids.py, provide 1 file: +- file with all acc numbers of complete genome + </help> +</tool>