Mercurial > repos > dazeone > clonalframeml
changeset 6:c659b21964c9 draft
Uploaded
| author | dazeone |
|---|---|
| date | Mon, 15 Mar 2021 15:03:45 +0000 |
| parents | 14840a53e6db |
| children | b34a8459650d |
| files | clonalframeml.xml |
| diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clonalframeml.xml Mon Mar 15 15:03:45 2021 +0000 @@ -0,0 +1,37 @@ +<tool id="clonalframeMLtool" name="clonalframeML" version="1.0"> + <description>a software package that performs efficient inference of recombination in bacterial genomes</description> +<requirements> + <requirement type="package" version="1.12">clonalframeml</requirement> +</requirements> + +<command>ClonalFrameMLold $input $input1 $output ; mv $output'.ML_sequence.fasta' $output ; mv $output'.labelled_tree.newick' $output1 ; mv $output'.em.txt' $output2 </command> + <inputs> + <param format="newick" name="input" type="data" label="Newick file : " multiple="false" display="checkboxes"/> + <param format="fasta" name="input1" type="data" label="Alignement fasta file : " multiple="false" display="checkboxes"/> + + </inputs> + + <outputs> + <data format="fasta" name="output" label="reduced Fasta Alignment" /> + <data format="newick" name="output1" label="labelled newick tree" /> + <data format="tabular" name="output2" label="em.txt" /> + </outputs> + + <tests> + <test> + <param name="input" value="tree_45ind_190kSNP.withST.nwk" /> + <param name="input" value="190ksnp_alignment_KP2.fa" /> + <output name="output" file="results.txt" /> + </test> +</tests> + + <help> +For full documentation, please go to the ClonalframeML wiki (https://github.com/katholt/Kleborate/wiki) + </help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1004041</citation> + </citations> +</tool> + + +