annotate extract_tree_order.xml @ 2:eb980e8bb133 draft default tip

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 669399887aebfe546eae29022f446664d9b52d44"

<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="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>