<tool id="contig_scaff" name="contig_scaff" version="0.1"> 
    <description> : Join scaffolds unsing a tabulated file</description>  
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
		source $__tool_directory__/include_scaffremodler.sh ;
        python $__tool_directory__/contig_scaff.py
		--table $table
		--fasta $fasta
		--out $fasta_file
		--out_verif $tabulated_file
		
    </command>
    <inputs>
		<param name="table" type="data" label="The table file of scaffold to join" />
		<param name="fasta" type="data" label="The multi-fasta scaffold file" />
		<param name="prefix" type="text" label="Identifier for output" />
    </inputs>
    <outputs>
        <data format="fasta" name="fasta_file" label="${tool.name} : $prefix fasta" />
        <data format="txt" name="tabulated_file" label="${tool.name} : $prefix tabulated" />
    </outputs>
    <help>
    
**Overview**

-----

.. class:: infomark

**Galaxy integration** Martin Guillaume (CIRAD), Droc Gaetan (CIRAD).

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to galaxy-dev-southgreen@cirad.fr

.. class:: infomark

**Program encapsulated in Galaxy by South Green**

	</help>
	<citations>
        <citation type="doi">10.1186/s12864-016-2579-4</citation> 
    </citations>
</tool>