annotate tree_relabeler.xml @ 2:41ada87567a2 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 8ad15943a8d365b3924ff7a5e53308cc56d7a6af

<tool id="tree_relabel" name="Tree Relabeler" version="1.1.0">
    <description>Relabels the tips of a newick formatted tree.</description>

    <requirements>
        <requirement type="package" version="1.7.2">perl-bioperl</requirement>
        <requirement type="package" version="2.49">perl-getopt-long</requirement>
    </requirements>
  <command detect_errors="exit_code">
    <![CDATA[
             $__tool_directory__/nml_tree_relabeler.pl -i '$treefile' -t '$tabfile' -o '$output' -d '$delim' $replace
    ]]>
  </command>
    <inputs>
        <param name="treefile" type="data" format="nhx" label="The newick formated tree file to be relabeled:" optional="false"/>
        <param name="tabfile" type="data" format="txt" label="The tab separated file containing the current labels and the info to be added to the labels" optional="false"/>
        <param name="delim" type="text" label="Delimiter for new tip labels (space, _, etc)" optional="true" help="If left blank, labels of updated tips will be separated by spaces."/>
        <param name="replace" truevalue='--replace' falsevalue='' type="boolean" label="Find and Replace current tip"  help="If false, will append to current tip. If true, will replace current tip"/>
    </inputs>

    <outputs>
        <data format="txt" name="output"/>
    </outputs>

    <tests>
        <test>
            <param name="treefile" value="phylogeneticTree.newick.nhx"/>
	    <param name="tabfile" value="tabs.txt"/>
	    <output name="output" file="results"/> 
        </test>
        <test>
            <param name="treefile" value="phylogeneticTree.newick.nhx"/>
	    <param name="tabfile" value="replacedtabs.txt"/>
            <param name="replace" value="true"/>
	    <output name="output" file="replacedresults"/>
        </test>
    </tests>
    <help>

What it does
============

This tool provides a means for relabeling the tips of a newick formatted tree.

It takes a newick format tree file to modify tip labels and a tab-delimited file containing current tip labels and additional information to add to the tips in 2 or more columns. 

Usage
=====

Header row of the tab delimited file must start with a '#'. An example is below:

- #label outbreak    year    location
- orgs1  outbreak1   year1   location1
- orgs2  outbreak2   year2   location2

and so on.

The information in the tab file is inserted into the tree file so the new information will appear on the tip labels.


Input
=====

Newick format tree

Tab delimted file

Desired delimiter for updated tip labels

    </help>
    <citations>
    </citations>
</tool>