<tool id="rename_scaffold" name="rename the scaffolds" version="1.2">
    <description>a Galaxy tool to rename the scaffolds in the reference genome so that they won't exceed 31 characters</description>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    python $__tool_directory__/rename.py $input $output $index
]]></command>
<inputs>
    <param name="input" type="data" format="fasta"/>
</inputs>
<outputs>
    <data name="output" format="fasta" label="${tool.name} on ${on_string}: renamed_reference" />
    <data name="index" format="csv" label="${tool.name} on ${on_string}: name mapping"/>
</outputs>
<tests>
    <test>
        <!-- Test with Dbia3.fa -->
        <param name="input" value="Dbia3.fa" />
        <output name="output" file="Dbia3_renamed.fa"/>
        <output name="index" file="Dbia3_index.csv"/>
    </test>
</tests>
<help><![CDATA[
This tool is to rename scaffolds in the reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and also output a name mapping file

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