Mercurial > repos > padge > phykit
comparison phykit_alignment_tree_based.xml @ 0:37b049bf729a draft
"planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
| author | padge |
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| date | Mon, 28 Mar 2022 16:23:18 +0000 |
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| -1:000000000000 | 0:37b049bf729a |
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| 1 <tool id="phykit_alignment_tree_based" name="PhyKit - Alignment- and tree-based functions" version="0.1.0" python_template_version="3.5"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.11.7">phykit</requirement> | |
| 4 </requirements> | |
| 5 <command detect_errors="exit_code"><![CDATA[ | |
| 6 #if $tools.tool_selector == "treeness_over_rcv" | |
| 7 phykit treeness_over_rcv -a $tools.input1 -t $tools.input2 > $treeness_rcv; | |
| 8 #end if | |
| 9 | |
| 10 | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <conditional name="tools"> | |
| 14 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)"> | |
| 15 <option value="treeness_over_rcv">Calculate treeness/RCV for a given alignment and tree.</option> | |
| 16 </param> | |
| 17 <when value="treeness_over_rcv"> | |
| 18 <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" /> | |
| 19 <param name="input2" type="data" format="newick" multiple="false" label="Tree file" optional="false" /> | |
| 20 </when> | |
| 21 </conditional> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="treeness_rcv" format="tabular" label="Three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV" > | |
| 25 <filter>tools['tool_selector']=='treeness_over_rcv'</filter> | |
| 26 </data> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="tool_selector" value="treeness_over_rcv" /> | |
| 31 <param name="input1" value="simple.fa"/> | |
| 32 <param name="input2" value="tree_simple.tre"/> | |
| 33 <output name="treeness_rcv" file="test_treeness_over_rcv.txt"/> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help><![CDATA[ | |
| 37 | |
| 38 Version: 1.11.3 | |
| 39 Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096 | |
| 40 Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-and-tree-based-functions | |
| 41 Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675 | |
| 42 | |
| 43 PhyKIT helps process and analyze multiple sequence alignments and phylogenies. | |
| 44 | |
| 45 Generally, all functions are designed to help understand the contents of alignments | |
| 46 (e.g., gc content or the number of parsimony informative sites) and the shape | |
| 47 of trees (e.g., treeness, degree of violation of a molecular clock). | |
| 48 | |
| 49 | |
| 50 Alignment- and tree-based commands | |
| 51 ================================== | |
| 52 treeness_over_rcv (alias: toverr) | |
| 53 - calculates treeness/rcv, treeness, and rcv | |
| 54 | |
| 55 ]]></help> | |
| 56 <citations> | |
| 57 <citation type="bibtex"> | |
| 58 @misc{githubPhyKIT, | |
| 59 author = {LastTODO, FirstTODO}, | |
| 60 year = {TODO}, | |
| 61 title = {PhyKIT}, | |
| 62 publisher = {GitHub}, | |
| 63 journal = {GitHub repository}, | |
| 64 url = {https://github.com/JLSteenwyk/PhyKIT}, | |
| 65 }</citation> | |
| 66 </citations> | |
| 67 </tool> |