Mercurial > repos > dcouvin > resfinder
view ResFinder.xml @ 0:a16d245332d6 draft default tip
Uploaded
author | dcouvin |
---|---|
date | Wed, 08 Dec 2021 01:46:07 +0000 |
parents | |
children |
line wrap: on
line source
<tool id="resfinder" name="ResFinder" version="4.0"> <description>identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.</description> <requirements> <requirement type="package" version="0.8.9">tabulate</requirement> <requirement type="package" version="1.79">biopython</requirement> <requirement type="package" version="1.5.6">cgecore</requirement> <requirement type="package" version="3.1.24">gitpython</requirement> <requirement type="package" version="2.8.2">python-dateutil</requirement> <requirement type="package" version="2.34.1">git</requirement> <requirement type="package" version="3.0.5">gcg</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re ## Creates symlinks for each input file based on the Galaxy 'element_identifier' ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') ## Add single quotes around each input file identifier #set $_input_file = "'{}'".format($input.element_identifier) ln -s '${input}' ${_input_file} && $__tool_directory__/resfinder/run_resfinder.py -s "$s" -l 0.6 -t 0.8 --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>