<tool id="AGEseq" name="AGEseq">
   <description>Analysis of Genome Editing by Sequencing</description>
   <command interpreter="perl">AGEseq_web.pl  $target  $read  $mismatch  $minAbundance  $wtNum  $indelNum  $output </command>
   <inputs>
     <param format="txt" name="target" type="data" label="Target File (Reference Table)" help="Select target/reference file."/>
     <param format=""   name="read"  type="data"  label="Read file (Sanger or NGS)" help="Select read file in fasta or fastq format." />
    

      <param name="mismatch" type="float" value="0.1" label="Mismatch Rate Cutoff" help="Mismatch rate to filter low quality alignment, default 0.1 (10 %)" />
      <param name="minAbundance" type="integer" value="0" label="Abundance Cutoff" help="Cutoff to filter reads with low abundance, default  0" />
      <param name="wtNum" type="integer" value="20" label="Number of WT-like records to be reported" help="Report top xx WT like records, default 20" />
      <param name="indelNum" type="integer" value="50" label="Number of records with indel(s) to be reported" help="Report top xx records with indel(s), default 50" />

   </inputs>

   <outputs>
     <data format="txt" name="output" />
   </outputs>


   <tests>
      <test>
       <param name="target" value="targets.txt"/>
       <param name="read" value="read_test.fastq"/>
       <output name="output" file="AGEseq_output.txt"/>
      </test>
   </tests>


   <help>
**AGEseq** compares amplicon sequences with expected target sequences and finds the insertion/deletion sites in the amplicon sequences.

Please refer to http://aspendb.uga.edu/downloads or https://github.com/liangjiaoxue/AGEseq for more details.


   </help>
 
 </tool>