view example2.xml @ 0:47e1dc8b27f8 draft

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<tool id="formatplotfasta" name="Adjust fasta line length and plot content" version="0.0.1" force_history_refresh="True">
  
  <description>Change the number of nucleotides per line in the input fasta and plot nt content </description>
  
  <requirements>
      <requirement type="package" version="1.4"> matplotlib </requirement>
  </requirements>

  <command interpreter="python"> example2.py "${infasta}" $linesize $formatted_fasta $plot </command>
  
  <inputs>
    <param name="infasta" format="fasta" type="data" label="input fasta" help="no help"/>
    <param name="linesize" type="integer" value="50" label="number of nt per line" help=" be reasonable!"/>
  </inputs>

  <outputs>
    <data name="formatted_fasta" format="fasta" label="${tool.name} on ${on_string}: formatted fasta"/>
    <data name="plot" format="pdf" label="${tool.name} on ${on_string}: plot"/>
  </outputs>

  <tests>
    <test>
      <param name="infasta" value="mouse_reference_mtDNA.fasta"/>
      <param name="linesize" value="200"/>
      <output name="formatted_fasta" file="adjusted_200_mouse_reference_mtDNA.fasta"/>
      <output name="plot" file="mouse_reference_mtDNA.fasta_nt_counts.pdf"/>
    </test>
  </tests>

  <help>
    
<![CDATA[
Short description.

-----

.. class:: infomark

**What it does**

Longer description. 

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.. class:: warningmark

**Note**

Some warining, if needed:

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.. class:: infomark

**Formats**

**FASTA multiple alignment** 

See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format

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**Example**


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**Citation**

(boris-at-bx.psu.edu) ]]>

  </help>
</tool>