Mercurial > repos > p.lucas > resfinder
changeset 0:e94c6265e7e1 draft
Uploaded wrapper
author | p.lucas |
---|---|
date | Wed, 06 Apr 2022 16:11:02 +0000 |
parents | |
children | 1ba09e41181d |
files | Resfinder_wrapper.xml |
diffstat | 1 files changed, 161 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Resfinder_wrapper.xml Wed Apr 06 16:11:02 2022 +0000 @@ -0,0 +1,161 @@ +<tool id="Resfinder" name="Resfinder" version="0"> + <description> + Resfinder: Identifcation of acquired antibiotic resistance genes + </description> + <requirements> + <requirement type="package" version="0.1">_libgcc_mutex</requirement> + <requirement type="package" version="4.5">_openmp_mutex</requirement> + <requirement type="package" version="1.78">biopython</requirement> + <requirement type="package" version="2.10.1">blast</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="1.17.1">c-ares</requirement> + <requirement type="package" version="2020.12.5">ca-certificates</requirement> + <requirement type="package" version="2020.12.5">certifi</requirement> + <requirement type="package" version="1.5.6">cgecore</requirement> + <requirement type="package" version="7.75.0">curl</requirement> + <requirement type="package" version="13.9">entrez-direct</requirement> + <requirement type="package" version="2.2.10">expat</requirement> + <requirement type="package" version="4.0.5">gitdb</requirement> + <requirement type="package" version="3.1.14">gitpython</requirement> + <requirement type="package" version="1.3.13">kma</requirement> + <requirement type="package" version="1.17.2">krb5</requirement> + <requirement type="package" version="2.35.1">ld_impl_linux-64</requirement> + <requirement type="package" version="3.9.0">libblas</requirement> + <requirement type="package" version="3.9.0">libcblas</requirement> + <requirement type="package" version="7.75.0">libcurl</requirement> + <requirement type="package" version="3.1.20191231">libedit</requirement> + <requirement type="package" version="4.33">libev</requirement> + <requirement type="package" version="3.3">libffi</requirement> + <requirement type="package" version="9.3.0">libgcc-ng</requirement> + <requirement type="package" 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version="3.9">python_abi</requirement> + <requirement type="package" version="8.0">readline</requirement> + <requirement type="package" version="49.6.0">setuptools</requirement> + <requirement type="package" version="1.15.0">six</requirement> + <requirement type="package" version="3.0.5">smmap</requirement> + <requirement type="package" version="3.34.0">sqlite</requirement> + <requirement type="package" version="0.8.9">tabulate</requirement> + <requirement type="package" version="8.6.10">tk</requirement> + <requirement type="package" version="2021">tzdata</requirement> + <requirement type="package" version="0.36.2">wheel</requirement> + <requirement type="package" version="5.2.5">xz</requirement> + <requirement type="package" version="1.2.11">zlib</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '${input}' ${_input_file} && python3 $__tool_directory__/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$y" --acquired --point -ifa $_input_file -db_res $__tool_directory__/resfinder/db_resfinder/ -db_point $__tool_directory__/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes + ]]></command> + <inputs> + <param format="fasta" name="input" type="data" label="FASTA file : "/> + <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist"> + <option value="campylobacter">Campylobacter spp.*</option> + <option value="campylobacter jejuni">Campylobacter jejuni*</option> + <option value="campylobacter coli">Campylobacter coli*</option> + <option value="escherichia coli">Escherichia coli*</option> + <option value="salmonella">Salmonella spp.*</option> + <option value="plasmodium falciparum">Plasmodium falciparum*</option> + <option value="neisseria gonorrhoeae">Neisseria gonorrhoeae*</option> + <option value="mycobacterium tuberculosis">Mycobacterium tuberculosis*</option> + <option value="enterococcus faecalis">Enterococcus faecalis*</option> + <option value="enterococcus faecium">Enterococcus faecium*</option> + <option value="klebsiella">Klebsiella*</option> + <option value="helicobacter pylori">Helicobacter pylori*</option> + <option value="staphylococcus aureus">Staphylococcus aureus*</option> + <option value="other">Other</option> + </param> + <param name="l" type="text" area="false" value="0.6" label="Minimum (breadth-of) coverage of ResFinder within the range 0-1:"/> + <param name="t" type="text" value="0.8" area="false" label="Threshold for identity of ResFinder within the range 0-1:"/> + </inputs> + <outputs> + <collection name="outputreport" type="list" label="${tool.name}: Report files"> + <discover_datasets pattern="(?P<name>.+)\.txt$" directory="./output" format="txt"/> + </collection> + <data format="fasta" name="resistance_genes" label="${tool.name}: resistance genes"/> + </outputs> + <help><![CDATA[ + This tool allows to identify acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria (in FASTA format). + + BitBucket: https://bitbucket.org/genomicepidemiology/resfinder/src/master/ + ]]></help> + + <citations> + <citation type="doi">10.1093/jac/dkaa345</citation> + </citations> +</tool>