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"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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<?xml version="1.0"?> <tool id="patrist" name="PATRIST" version="@VERSION@"> <description>extract patristic distance from a tree</description> <macros> <token name="@VERSION@">0.1.2</token> </macros> <requirements> <requirement type="package" version="3.8.0">python</requirement> <requirement type="package" version="1.74">biopython</requirement> </requirements> <version_command>python '$__tool_directory__/patrist.py'</version_command> <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/patrist.py' #if '$minimize': --minimize #end if #if '$keep_ties': --keep_ties #end if --overwrite '$tree' '$cutoff' '$outfile' ]]> </command> <inputs> <param format="nhx" name="tree" type="data" multiple="false" label="Newick tree file" /> <param name="cutoff" type="float" value="0.5" label="Maximum patristic distance" /> <param name="minimize" type="boolean" truevalue="" falsevalue="" checked="false" label="Report no more than one nearest neighbour per tip" /> <param name="keep_ties" type="boolean" truevalue="" falsevalue="" checked="false" label="If more than one tip has the same patristic distance report all as nearest neighbours" /> </inputs> <outputs> <data name="outfile" format="csv" label="${tool.name} on ${on_string}:outfile.csv" /> </outputs> <tests> <test> <param name="tree" value="tree.nhx" /> <param name="cutoff" value="0.5" /> <output name="outfile" file="outfile.csv" ftype="csv" lines_diff="0" /> </test> </tests> <help> <![CDATA[ =========== Description =========== .. class:: infomark Patrist will rapidly extract patristic distances from a tree for clustering tips below a user-defined threshold. .. _Patrist: https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 ----- Input ----- 'tree', <input> file containing Newick tree string. ---------- Parameters ---------- 'cutoff', Maximum patristic distance. '--minimize', Report no more than one nearest neighbour per tip. '--keep_ties', If more than one tip has the same patristic distance report all as nearest neighbours. ------ Output ------ 'outfile', <output> file to write results in CSV format.' The script overwrites any file with the current file name in the output directory. ]]> </help> <citations> </citations> </tool>