Mercurial > repos > nml > patrist
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/patrist.xml Tue Dec 17 09:53:52 2019 -0500 @@ -0,0 +1,81 @@ +<?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>