Mercurial > repos > nml > patrist
comparison patrist.xml @ 0:f8847f5a5491 draft default tip
"planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
| author | nml |
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| date | Tue, 17 Dec 2019 09:53:52 -0500 |
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| -1:000000000000 | 0:f8847f5a5491 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="patrist" name="PATRIST" version="@VERSION@"> | |
| 3 <description>extract patristic distance from a tree</description> | |
| 4 <macros> | |
| 5 <token name="@VERSION@">0.1.2</token> | |
| 6 </macros> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="3.8.0">python</requirement> | |
| 9 <requirement type="package" version="1.74">biopython</requirement> | |
| 10 </requirements> | |
| 11 <version_command>python '$__tool_directory__/patrist.py'</version_command> | |
| 12 <command detect_errors="aggressive"> | |
| 13 <![CDATA[ | |
| 14 python '$__tool_directory__/patrist.py' | |
| 15 | |
| 16 #if '$minimize': | |
| 17 --minimize | |
| 18 #end if | |
| 19 #if '$keep_ties': | |
| 20 --keep_ties | |
| 21 #end if | |
| 22 --overwrite | |
| 23 | |
| 24 '$tree' '$cutoff' '$outfile' | |
| 25 ]]> | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param format="nhx" name="tree" type="data" multiple="false" label="Newick tree file" /> | |
| 29 <param name="cutoff" type="float" value="0.5" label="Maximum patristic distance" /> | |
| 30 <param name="minimize" type="boolean" truevalue="" falsevalue="" checked="false" label="Report no more than one nearest neighbour per tip" /> | |
| 31 <param name="keep_ties" type="boolean" truevalue="" falsevalue="" checked="false" label="If more than one tip has the same patristic distance report all as nearest neighbours" /> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="outfile" format="csv" label="${tool.name} on ${on_string}:outfile.csv" /> | |
| 35 </outputs> | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="tree" value="tree.nhx" /> | |
| 39 <param name="cutoff" value="0.5" /> | |
| 40 <output name="outfile" file="outfile.csv" ftype="csv" lines_diff="0" /> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help> | |
| 44 <![CDATA[ | |
| 45 | |
| 46 =========== | |
| 47 Description | |
| 48 =========== | |
| 49 | |
| 50 .. class:: infomark | |
| 51 | |
| 52 Patrist will rapidly extract patristic distances from a tree for clustering tips | |
| 53 below a user-defined threshold. | |
| 54 | |
| 55 .. _Patrist: https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 | |
| 56 | |
| 57 ----- | |
| 58 Input | |
| 59 ----- | |
| 60 | |
| 61 'tree', <input> file containing Newick tree string. | |
| 62 | |
| 63 ---------- | |
| 64 Parameters | |
| 65 ---------- | |
| 66 | |
| 67 'cutoff', Maximum patristic distance. | |
| 68 '--minimize', Report no more than one nearest neighbour per tip. | |
| 69 '--keep_ties', If more than one tip has the same patristic distance report all as nearest neighbours. | |
| 70 | |
| 71 ------ | |
| 72 Output | |
| 73 ------ | |
| 74 | |
| 75 'outfile', <output> file to write results in CSV format.' The script overwrites any file with the current file name in the output directory. | |
| 76 | |
| 77 ]]> | |
| 78 </help> | |
| 79 <citations> | |
| 80 </citations> | |
| 81 </tool> |