diff emboss_5/emboss_showfeat.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_showfeat.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0">
+  <!-- tool gives memory errors -->
+  <description>Show features of a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <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 format="data" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="html_out1" type="select">
+      <label>Format output as an HTML table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="matchsource" size="50" type="text" value="*">
+      <label>Feature source to match</label>
+    </param>
+    <param name="matchtype" size="50" type="text" value="*">
+      <label>Feature type to match</label>
+    </param>
+    <param name="matchtag" size="50" type="text" value="*">
+      <label>Feature tags to match</label>
+    </param>
+    <param name="matchvalue" size="50" type="text" value="*">
+      <label>Tag values to match</label>
+    </param>
+    <param name="sort" type="select">
+      <label>Sort by</label>
+      <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" size="50" type="text" value="">
+      <label>Regions to annotate by marking</label>
+    </param>
+    <param name="id" type="select">
+      <label>Display the ID name of the sequence</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="description" type="select">
+      <label>Display the description of the sequence</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="scale" type="select">
+      <label>Display the scale line</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="width" size="50" type="text" value="60">
+      <label>Screen width</label>
+    </param>
+    <param name="collapse" type="select">
+      <label>Collapse features</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="forward" type="select">
+      <label>Display forward sense features</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="reverse" type="select">
+      <label>Display reverse sense features</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="unknown" type="select">
+      <label>Display unknown sense features</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="strand" type="select">
+      <label>Display the strand of the features</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="source" type="select">
+      <label>Display the source of the features</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="position" type="select">
+      <label>SDisplay the start and end position of the features</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="type" type="select">
+      <label>Display the type of the features</label>
+      <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</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="values" type="select">
+      <label>Display the tag values of the features</label>
+      <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</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="showfeat" name="out_file1" />
+  </outputs>
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.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>
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