annotate patrist.xml @ 0:f8847f5a5491 draft default tip

"planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"

<?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>