<?xml version="1.0"?>
<tool id="msaboot" name="MSABOOT" version="@VERSION@">
    <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description>
    <macros>
        <token name="@VERSION@">0.1.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">msaboot</requirement>
    </requirements>
    <version_command>msaboot --version</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
msaboot -i '$input' -n $number -o '$output'
#if $save_logfile:
    > '$log' 2>&1
#end if
        ]]>
    </command>
    <inputs>
        <param name="input" format="fasta" type="data" label="FASTA input file" />
        <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." />
        <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" />
    </inputs>
    <outputs>
        <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" />
        <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt">
            <filter>save_logfile</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="msa.fasta" />
            <param name="number" value="10" />
            <param name="save_logfile" value="true" />
            <output name="log" file="log.txt" ftype="txt" compare="contains" />
            <output name="output" file="out.phylip" ftype="phylip" compare="contains" />
        </test>
    </tests>
    <help>
<![CDATA[

===========
Description
===========

.. class:: infomark

A tool for creating bootstrapping replicates from Multiple Sequence Alignment data.

.. _msaboot: https://github.com/phac-nml/msaboot

-----

-----
Input
-----
Input file location of FASTA file containing Multiple Sequence Alignment data(-i)

----------
Parameters
----------
Number of bootstrapping replicates (-n)

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

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

(A) The bootstrapped replicates in Phylip format.

(B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data.

]]>
    </help>
    <citations>
        <citation type="bibtex">
            @misc{GitHubmsaboot,
            title = {msaboot},
            publisher = {phac-nml},
            journal = {GitHub repository},
            url = {https://github.com/phac-nml/msaboot},
            }
        </citation>
    </citations>
</tool>