Mercurial > repos > dcouvin > pmlst
diff pmlst.xml @ 0:6dcb66689a7d draft default tip
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author | dcouvin |
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date | Wed, 25 Aug 2021 21:12:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst.xml Wed Aug 25 21:12:34 2021 +0000 @@ -0,0 +1,49 @@ +<tool id="pmlst" name="pmlst" version="2.0"> + <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description> + + + <requirements> + <requirement type="package" version="3.2.0">python3-openid</requirement> + <requirement type="package" version="21.2.4">pip</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.5.6">cgecore</requirement> + <requirement type="package" version="0.8.9">tabulate</requirement> + </requirements> + + + <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>--> + + <command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Select FASTA files: " /> + + <param name="s" type="select" label="Scheme database used for pMLST prediction:"> + + <option value="incac">incac</option> + <option value="incf">incf</option> + <option value="inchi1">inchi1</option> + <option value="inchi2">inchi2</option> + <option value="inci1">inci1</option> + <option value="incn">incn</option> + <option value="pbssb1-family">pbssb1-family</option> + + </param> + + + </inputs> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + + </help> + <citations> + <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> + </citations> +</tool> + + +