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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit a7380cf90205de589a64fe0105ea957402d62300"
author brinkmanlab
date Tue, 16 Jun 2020 12:50:07 -0400
parents e9f04f5172e4
children eb980e8bb133
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<tool id="extract-tree-order" name="BioPython Phylo Parse Newick Leaf Order" version="1.0" profile="16.04">
    <description>Convert a newick tree to an ordered list of its leaves</description>
    <edam_topics>
        <edam_topic>topic_0084</edam_topic>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0326</edam_operation>
        <edam_operation>operation_3434</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="1.76">biopython</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python -c \$'from Bio import Phylo\nfor clade in Phylo.read("$input", "newick").get_terminals(order="preorder"): print(clade.name)' > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="newick" label="Input" />
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="test-data/test.newick" ftype="newick" />
            <output name="output" file="test-data/output.txt" ftype="txt" />
        </test>
    </tests>
    <help><![CDATA[
        Convert a newick tree to an ordered list of its leaves as determined by BioPython.Phylo 'preorder'.
        
        This is useful when tree order affects order of processing of the related data.
        
        For example, you may want to do pairwise alignment of the sequences for adjacent leaves.
        
        `('NC_008463':1.25269,('NC_002516':0.21042,'NC_018080':0.20913)0.940:0.00444,('NZ_CH482384':0.24749,('NC_011770':0.00035,('NZ_CP006982':0.00036,'NC_023066':0.00018)0.940:0.00019)1.000:0.18245)0.990:0.01335);`
        
        returns
        
        ```
        NC_008463
        NC_002516
        NC_018080
        NZ_CH482384
        NC_011770
        NZ_CP006982
        NC_023066
        ```
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3364789</citation>
    </citations>
</tool>