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<?xml version="1.0"?>
<tool id="ucsc_trix_index_generator" name="UCSC Trix Index Generator" version="1.0">
    <description>Create UCSC Trix index from a tab-delimited text file or a Fasta file</description>
    <requirements>
        <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $input_type.input_type_selector == "fasta":
            python $__tool_directory__/extractHeaders.py $input_type.input_file tab_file
            &&
            ixIxx tab_file ${index_ix} ${index_ixx}
        #else:
            ixIxx $input_type.input_file ${index_ix} ${index_ixx}
        #end if
]]></command>
    <inputs>
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Choose the format" argument="--file_type">
                <option value="tab">Tabular</option>
                <option value="fasta" selected="True">Fasta</option>
            </param>
            <when value="tab">
                <param name="input_file" type="data" format="tabular" label="Tabular File" argument="-f"/>
            </when>
            <when value="fasta">
                <param name="input_file" type="data" format="fasta" label="Fasta File" argument="-f"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="trix_index" type="list" label="${tool.name} on ${on_string}:Trix index">
            <data name="index_ix" format="txt" />
            <data name="index_ixx" format="txt" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_type_selector" value="fasta" />
            <param name="input_file" value="dmel-hits-translation-r6.11.fasta" />
            <output_collection name="trix_index" type="list">
                <element name="index_ix" value="out.ix" />
                <element name="index_ixx" value="out.ixx" />
            </output_collection>
        </test>
        <test>
            <param name="input_type_selector" value="tab" />
            <param name="input_file" value="dmel-hits-tab" />
            <output_collection name="trix_index" type="list">
                <element name="index_ix" value="out.ix" />
                <element name="index_ixx" value="out.ixx" />
            </output_collection>
        </test>
    </tests> 
  <help>
        <![CDATA[
UCSC Trix Index Generator
==========================

Generate UCSC Trix index from a Fasta file or a Tabular file
-------------------------------------------------------------

ixIxx - Create indices for simple line-oriented file of format

Reference: https://genome.ucsc.edu/goldenpath/help/trix.html

Source code:
============

http://hgdownload.cse.ucsc.edu/admin/exe/

]]></help> 
 <citations>
    <citation type="bibtex">
@article{Kent01062002,
author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler,  and David},
title = {The Human Genome Browser at UCSC},
volume = {12},
number = {6},
pages = {996-1006},
year = {2002},
doi = {10.1101/gr.229102},
URL = {http://genome.cshlp.org/content/12/6/996.abstract},
eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
journal = {Genome Research}
}
    </citation>
</citations> 
</tool>