mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
72 lines
3.3 KiB
XML
72 lines
3.3 KiB
XML
<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
|
|
<description>Find differences between nearly identical sequences</description>
|
|
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
<command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize '$wordsize' -globaldifferences '$globaldifferences' -rformat3
|
|
'$out_format1' -offormat4 '$out_format2' -offormat5 '$out_format3' -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="20">
|
|
<label>Wordsize</label>
|
|
</param>
|
|
<param name="globaldifferences" type="select">
|
|
<label>Report differences at the ends</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="out_format1" type="select">
|
|
<label>Output Report File Format</label>
|
|
<option value="diffseq">Diffseq</option>
|
|
<option value="embl">EMBL</option>
|
|
<option value="genbank">GENBANK</option>
|
|
<option value="gff">GFF</option>
|
|
<option value="pir">PIR</option>
|
|
<option value="swiss">SwissProt</option>
|
|
<option value="dbmotif">DbMotif</option>
|
|
<option value="excel">Excel (tab delimited)</option>
|
|
<option value="feattable">FeatTable</option>
|
|
<option value="motif">Motif</option>
|
|
<option value="regions">Regions</option>
|
|
<option value="seqtable">SeqTable</option>
|
|
<option value="simple">SRS Simple</option>
|
|
<option value="srs">SRS</option>
|
|
<option value="table">Table</option>
|
|
<option value="tagseq">TagSeq</option>
|
|
</param>
|
|
<param name="out_format2" type="select">
|
|
<label>Sequence 1 Output Feature File Format</label>
|
|
<option value="gff">GFF</option>
|
|
<option value="embl">EMBL</option>
|
|
<option value="swiss">SwissProt</option>
|
|
</param>
|
|
<param name="out_format3" type="select">
|
|
<label>Sequence 2 Output Feature File Format</label>
|
|
<option value="gff">GFF</option>
|
|
<option value="embl">EMBL</option>
|
|
<option value="swiss">SwissProt</option>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="diffseq" name="out_file1" />
|
|
<data format="gff" name="out_file2" />
|
|
<data format="gff" name="out_file3" />
|
|
</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/diffseq.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> |