annotate emboss_lindna.xml @ 17:ce385837c160 draft

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

<tool id="EMBOSS: lindna48" name="lindna" version="@VERSION@.1">
  <!-- tool produces memory error in ajmem.c -->
  <description>Draws linear maps of DNA constructs</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="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 name="input1" type="data" format="data" label="Sequences" />
    <param name="ruler" type="select" label="Draw a ruler">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="blocktype" type="select" label="Type of blocks">
      <option value="Filled">Filled blocks</option>
      <option value="Open">Open blocks</option>
      <option value="Outline">Black border</option>
    </param>
    <param name="maxgroups" type="integer" value="20" label="Maximum number of groups" />
    <param name="maxlabels" type="integer" value="10000" label="Maximum number of labels" />
    <param name="intersymbol" type="select" label="Type of blocks">
      <option value="Straight">Straight</option>
    </param>
    <param name="intercolour" type="select" label="Colour of junctions between blocks">
      <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">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="gapsize" type="integer" value="500" label="Interval between ticks in the ruler" />
    <param name="ticklines" type="select" label="Vertical lines at the ruler's ticks">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="textheight" type="float" value="1.0" label="Height of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="textlength" type="float" value="1.0" label="Length of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="margin" type="float" value="1.0" label="Width of left margin" help="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" />
    <param name="tickheight" type="float" value="1.0" label="Height of ticks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="blockheight" type="float" value="1.0" label="Height of blocks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="rangeheight" type="float" value="1.0" label="Height of range ends" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="gapgroup" type="float" value="1.0" label="Space between groups" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
    <param name="postext" type="float" value="1.0" label="Space between text and ticks, blocks, and ranges" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
  </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/lindna.html
  </help>
  <expand macro="citations" />
</tool>