Mercurial > repos > dazeone > clonalframeml
comparison clonalframeml.xml @ 8:0afb951f32b0 draft
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| author | dazeone |
|---|---|
| date | Mon, 15 Mar 2021 15:16:44 +0000 |
| parents | def4c8a61e22 |
| children | 3723163ffed7 |
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| 7:b34a8459650d | 8:0afb951f32b0 |
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| 1 <tool id="clonalframeMLtool" name="clonalframeML" version="1.0"> | |
| 2 <description>a software package that performs efficient inference of recombination in bacterial genomes</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.12">clonalframeml</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <command>ClonalFrameML $input $input1 $output ; mv $output'.ML_sequence.fasta' $output ; mv $output'.labelled_tree.newick' $output1 ; mv $output'.em.txt' $output2 </command> | |
| 8 <inputs> | |
| 9 <param format="newick" name="input" type="data" label="Newick file : " multiple="false" display="checkboxes"/> | |
| 10 <param format="fasta" name="input1" type="data" label="Alignement fasta file : " multiple="false" display="checkboxes"/> | |
| 11 | |
| 12 </inputs> | |
| 13 | |
| 14 <outputs> | |
| 15 <data format="fasta" name="output" label="reduced Fasta Alignment" /> | |
| 16 <data format="newick" name="output1" label="labelled newick tree" /> | |
| 17 <data format="tabular" name="output2" label="em.txt" /> | |
| 18 </outputs> | |
| 19 | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="tree_45ind_190kSNP.withST.nwk" /> | |
| 23 <param name="input" value="190ksnp_alignment_KP2.fa" /> | |
| 24 <output name="output" file="results.txt" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 | |
| 28 <help> | |
| 29 For full documentation, please go to the ClonalframeML wiki (https://github.com/katholt/Kleborate/wiki) | |
| 30 </help> | |
| 31 <citations> | |
| 32 <citation type="doi">10.1371/journal.pcbi.1004041</citation> | |
| 33 </citations> | |
| 34 </tool> | |
| 35 | |
| 36 | |
| 37 |