comparison emboss_pepwheel.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
  <!-- produces png file -->
  <description>Shows protein sequences as helices</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
  $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="steps" type="text" value="18">
      <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
    </param>
    <param name="turns" type="text" value="5">
      <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
    </param>
    <param name="squares" type="text" value="ILVM">
      <label>Residues to mark with squares</label>
    </param>
    <param name="diamonds" type="text" value="DENQST">
      <label>Residues to mark with diamonds</label>
    </param>
    <param name="octags" type="text" value="HKR">
      <label>Residues to mark with octagons</label>
    </param>
    <param name="wheel" type="select">
      <label>Plot the wheel</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="amphipathic" type="select">
      <label>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</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="out_file1" />
  </outputs>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0.1">
  <!-- produces png file -->
  <description>Shows protein sequences as helices</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic
  $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="steps" type="integer" value="18" label="Steps, the number of residues plotted per turn is this value divided by the 'turns' value" />
    <param name="turns" type="integer" value="5" label="Turns, the number of residues plotted per turn is the 'steps' value divided by this value" />
    <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="wheel" type="select" label="Plot the wheel">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <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/pepwheel.html
  </help>
  <expand macro="citations" />
</tool>