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annotate phykit_alignment_tree_based.xml @ 0:37b049bf729a draft

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