view emboss_5/emboss_lindna.xml @ 8:b810c96613ee draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0">
  <!-- tool produces memory error in ajmem.c -->
  <description>Draws linear maps of DNA constructs</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
  -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
  $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="ruler" type="select">
      <label>Draw a ruler</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="blocktype" type="select">
      <label>Type of blocks</label>
      <option value="Filled">Filled blocks</option>
      <option value="Open">Open blocks</option>
      <option value="Outline">Black border</option>
    </param>
    <param name="maxgroups" type="text" value="20">
      <label>Maximum number of groups</label>
    </param>
    <param name="maxlabels" type="text" value="10000">
      <label>Maximum number of labels</label>
    </param>
    <param name="intersymbol" type="select">
      <label>Type of blocks</label>
      <option value="Straight">Straight</option>
    </param>
    <param name="intercolour" type="select">
      <label>Colour of junctions between blocks</label>
      <option value="1">Red</option>
      <option value="0">Black</option>
      <option value="2">Yellow</option>
      <option value="3">Green</option>
      <option value="4">Aquamarine</option>
      <option value="5">Pink</option>
      <option value="6">Wheat</option>
      <option value="7">Grey</option>
      <option value="8">Brown</option>
      <option value="9">Blue</option>
      <option value="10">Blue-violet</option>
      <option value="11">Cyan</option>
      <option value="12">Turquoise</option>
      <option value="13">Magenta</option>
      <option value="14">Salmon</option>
      <option value="15">White</option>
    </param>
    <param name="interticks" type="select">
      <label>Horizontal junctions between ticks</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="gapsize" type="text" value="500">
      <label>Interval between ticks in the ruler</label>
    </param>
    <param name="ticklines" type="select">
      <label>Vertical lines at the ruler's ticks</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="textheight" type="text" value="1.0">
      <label>Height of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="textlength" type="text" value="1.0">
      <label>Length of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="margin" type="text" value="1.0">
      <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size,
      respectively</label>
    </param>
    <param name="tickheight" type="text" value="1.0">
      <label>Height of ticks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="blockheight" type="text" value="1.0">
      <label>Height of blocks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="rangeheight" type="text" value="1.0">
      <label>Height of range ends. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="gapgroup" type="text" value="1.0">
      <label>Space between groups. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </param>
    <param name="postext" type="text" value="1.0">
      <label>Space between text and ticks, blocks, and ranges. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
    </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/lindna.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>