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view fasta_manual_input.xml @ 12:6b7d31026d1c draft

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author petr-novak
date Tue, 04 Feb 2020 08:38:22 -0500
parents c2c69c6090f0
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<tool id="fasta_input" name="Fasta interactive input" version="1.0.0">
  <description> Enter fasta file to text window </description>
  <command>
    echo "${fasta_text}" > ${fasta_file}  &amp;&amp;
    sed -i 's/__gt__/>/g' ${fasta_file}  &amp;&amp;
    sed -i 's/__cn__/\n/g' ${fasta_file}
  </command>

  <inputs>
    <param  type="text" name="fasta_text" area="True" size="50x150" label="Paste sequences in FASTA format" />
  </inputs>


  <outputs>
    <data format="fasta" name="fasta_file" label="FASTA sequence manually edited" />
  </outputs>

  <help>
    This is helper tool to enter fasta sequences manualy
  </help>
</tool>