annotate fasttree/fasttree.xml @ 0:b2b9795cc862 draft

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<tool name="FastTree" id="fasttree" version="2.17"> 
<description>FastTree - FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</description>
 <command>
	FastTree $format &lt; $input &gt; $output 2&gt; $log
</command>
 <requirements>
    <requirement type="package" version="2.17">FastTree</requirement>
  </requirements>
 <inputs>
  <param name="input" type="data" format="fasta" label="Aligned sequences file (FASTA format)" help="Aligment, e.g. from the 'PyNAST' tool"/>
  <param name="format" type="select" label="Nucleotide or protein alignment" help="Specify if the aligned sequences are nucleotide or protein sequences">
        <option value="-nt" selected="true">Nucleotide</option>
        <option value="">Protein</option>
  </param>
</inputs>
<outputs>
  <data name="output" format="nhx" type="nhx" label="${tool.name} on ${on_string}:tree.nhx" />
  <data name="log" format="txt" hidden="TRUE" type="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt" />
</outputs>
<tests>
  <test>
    <param name="input_file" value="seq.fna" />
    <param name="mode" value="-nt" />
    <output name="output" file="tree.nhx" ftype="txt" lines_diff="10" />
    <output name="log" file="log_FastTree_run.txt" ftype="txt" lines_diff="10" />
  </test>
</tests>
<help>
===========
Description
===========

.. class:: infomark

An additional file is generated by this tool, which is hidden from the history list. You can view these outputs by clicking on the cogwheel next to the "History Panel" and select "Include Hidden Dataset".

FastTree_ infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software.

.. _FastTree: http://meta.microbesonline.org/fasttree

-----

-----
Input
-----

A) Aligned sequences file in FASTA format, e.g. the alignment from the 'PyNAST' tool.

----------
Parameters
----------

Nucleotide or protein alignment
 To specify the type of sequence alignment (nucleotide or protein) you are providing.

------
Output
------

This tool produces two output files, one of which is hidden by default (the log file).

.. class:: infomark

You can view the hidden output by clicking on the cog wheel next to the History panel and select "Include Hidden Dataset".

(A) The phylogenetic tree in Newick_ format (nhx).

.. class:: infomark

 The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences.

(B) *(hidden)* The log file, containing information of the FastTree run to build the phylogenetic tree. 


.. _Newick: http://en.wikipedia.org/wiki/Newick_format

-----


=========
Resources
=========

FastTree_

.. _FastTree: http://meta.microbesonline.org/fasttree/#Install

**Wrapper Author**

QFAB Bioinformatics ([e-mail])
</help>
<tests>
  <test>
    <param name="input" value="aligned.fasta" />
    <param name="format" value="-nt" />
    <output name="output" file="tree.nhx" ftype="nhx" lines_diff="10" />
    <output name="log" file="log.txt" ftype="txt" lines_diff="10" />
  </test>
</tests>
</tool>