mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
44 lines
2.2 KiB
XML
44 lines
2.2 KiB
XML
<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
|
|
<description>Non-overlapping wordmatch dotplot of two sequences</description>
|
|
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
<command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize '$wordsize' -overlaps '$overlaps' -boxit '$boxit' -graph png
|
|
-auto</command>
|
|
<inputs>
|
|
<param format="data" name="input1" type="data">
|
|
<label>Sequence 1</label>
|
|
</param>
|
|
<param format="data" name="input2" type="data">
|
|
<label>Sequence 2</label>
|
|
</param>
|
|
<param name="wordsize" size="4" type="text" value="4">
|
|
<label>Word size (Integer 2 or more)</label>
|
|
</param>
|
|
<param name="overlaps" type="select">
|
|
<label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="boxit" type="select">
|
|
<label>Draw a box around dotplot</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="png" name="out_file1" />
|
|
</outputs>
|
|
<!-- functional tests not possible since image output contains file name information and timestamp -->
|
|
<help>
|
|
You can view the original documentation here_.
|
|
|
|
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
|
|
|
|
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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
|
|
</help>
|
|
</tool> |