/tools/emboss_5/emboss_helixturnhelix.xml

 1<tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0">
 2  <description>Report nucleic acid binding motifs</description>
 3  <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
 4  <inputs>
 5    <param format="data" name="input1" type="data">
 6      <label>Sequences</label>
 7    </param>
 8    <param name="mean" size="10" type="text" value="238.71">
 9      <label>Mean value</label>
10    </param>
11    <param name="sd" size="10" type="text" value="293.61">
12      <label>Standard Deviation value</label>
13    </param>
14    <param name="minsd" size="10" type="text" value="2.5">
15      <label>Minimum SD</label>
16    </param>
17    <param name="eightyseven" type="select">
18      <label>Use the old (1987) weight data</label>
19      <option value="no">No</option>
20      <option value="yes">Yes</option>
21    </param>
22    <param name="out_format1" type="select">
23      <label>Output Report File Format</label>
24      <option value="motif">Motif</option>
25      <option value="embl">EMBL</option>
26      <option value="genbank">GENBANK</option>
27      <option value="gff">GFF</option>
28      <option value="pir">PIR</option>
29      <option value="swiss">SwissProt</option>
30      <option value="dbmotif">DbMotif</option>
31      <option value="diffseq">Diffseq</option>
32      <option value="excel">Excel (tab delimited)</option>
33      <option value="feattable">FeatTable</option>
34      <option value="regions">Regions</option>
35      <option value="seqtable">SeqTable</option>
36      <option value="simple">SRS Simple</option>
37      <option value="srs">SRS</option>
38      <option value="table">Table</option>
39      <option value="tagseq">TagSeq</option>
40    </param>
41  </inputs>
42  <outputs>
43    <data format="motif" name="out_file1" />
44  </outputs>
45  <tests>
46    <test>
47      <param name="input1" value="2.fasta"/>
48      <param name="mean" value="238.71"/>
49      <param name="sd" value="293.61"/>
50      <param name="minsd" value="2.5"/>
51      <param name="eightyseven" value="no"/>
52      <param name="out_format1" value="excel"/>
53      <output name="out_file1" file="emboss_helixturnhelix_out.tabular"/>
54    </test>
55  </tests>
56  <code file="emboss_format_corrector.py" />
57  <help>
58    You can view the original documentation here_.
59    
60    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.html
61  </help>
62</tool>