annotate emboss_pepnet.xml @ 17:ce385837c160 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"

<tool id="EMBOSS: pepnet70" name="pepnet" version="@VERSION@">
  <!-- graphical output file with path information -->
  <description>Displays proteins as a helical net</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic $amphipathic -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" />
    <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" />
    <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" />
    <param name="amphipathic" type="select" label="Amphipathic?" help="If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="png" />
  </outputs>
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepnet.html
  </help>
  <expand macro="citations" />
</tool>