<tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.1">
<description>Generate DNA scaffold from blastx alignment of Contigs</description>
<requirements>
    <requirement type="package" version="3.7.6">python</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/blastx_to_scaffold.py
                              --sequences $sequences
                              --blastx-tab $blastx_tab
                              --output $output
]]></command>
<inputs>
<param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> 
<param name="blastx_tab"  type="data" format="tabular" label="Select a blastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> 

</inputs>
<outputs>
 <data format="fasta" name="output"/>
</outputs>


<tests>
  <test>
    <param name="sequences" value="contigs.fa" ftype="fasta"/>
    <param name="blastx_tab" value="blastx.tab" ftype="tabular"/>
    <output name="output" file="scaffold.fa" ftype="fasta"/>
  </test>
</tests>
        

<help>


**What it Does**
This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard
columns plus column 13 with the length of the blastx subject.

The final scaffold is a DNA sequence.

Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.

</help>

<citations>
    <citation type="doi">10.1186/s13742-015-0080-7</citation>
</citations>

</tool>