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Version 5.0 of EMBOSS Antigenic tool.

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Chinmay Rao
2007-12-11 15:59:01 +00:00
parent f7f7aeab26
commit 3539fb038d
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test-data/2.fasta
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>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
aacaattcta atggtcaaaa a
tools/emboss_5/emboss_antigenic.xml
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<tool id="EMBOSS_antigenic2" name="antigenic">
<description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
<command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>On query</label>
</param>
<param name="minlen" size="4" type="text" value="6">
<label>Minimum Length of region</label>
</param>
<param name="out_format1" type="select">
<label>Output format</label>
<option value="gff">GFF</option>
<option value="pir">PIR</option>
<option value="swiss">SwissProt</option>
<option value="dbmotif">DbMotif</option>
<option value="diffseq">diffseq</option>
<option value="excel">Excel (TAB Delimited)</option>
<option value="feattable">FeatTable</option>
<option value="motif">Motif</option>
<option value="nametable">NameTable</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>
<option value="antigenic">Antigenic Output File</option>
</param>
</inputs>
<outputs>
<data format="antigenic" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="minlen" value="6"/>
<param name="out_format1" value="excel"/>
<output name="out_file1" file="emboss_antigenic_out.tabular"/>
</test>
</tests>
<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/antigenic.html
</help>
</tool>