annotate emboss_showfeat.xml @ 13:8992d258e42f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: showfeat85" name="showfeat" version="@VERSION@.1">
  <!-- tool gives memory errors -->
  <description>Show features of a sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort $sort -annotation '$annotation' -id
  $id -description $description -scale $scale -width $width -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
  $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequences" />
    <param name="html_out1" type="select" label="Format output as an HTML table">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="matchsource" type="text" value="*" label="Feature source to match" />
    <param name="matchtype" type="text" value="*" label="Feature type to match" />
    <param name="matchtag" type="text" value="*" label="Feature tags to match" />
    <param name="matchvalue" type="text" value="*" label="Tag values to match" />
    <param name="sort" type="select" label="Sort by">
      <option value="start">Start position</option>
      <option value="source">Source</option>
      <option value="type">Type</option>
      <option value="nosort">No sorting done</option>
      <option value="join">Join coding regions together</option>
    </param>
    <param name="annotation" type="text" value="" label="Regions to annotate by marking" />
    <param name="id" type="select" label="Display the ID name of the sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="description" type="select" label="Display the description of the sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="scale" type="select" label="Display the scale line">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="width" type="integer" value="60" label="Screen width" />
    <param name="collapse" type="select" label="Collapse features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="forward" type="select" label="Display forward sense features">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="reverse" type="select" label="Display reverse sense features">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="unknown" type="select" label="Display unknown sense features">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="strand" type="select" label="Display the strand of the features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="source" type="select" label="Display the source of the features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="position" type="select" label="Display the start and end position of the features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="type" type="select" label="Display the type of the features">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="tags" type="select" label="Display the tags and values of the features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="values" type="select" label="Display the tag values of the features">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="stricttags" type="select" label="Display only those tag/value pairs in a feature that match the specified tag and value">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="showfeat" />
  </outputs>
  <help>
    You can view the original documentation here_.

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