/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  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequences</label>
 8    </param>
 9    <param name="mean" size="10" type="text" value="238.71">
10      <label>Mean value</label>
11    </param>
12    <param name="sd" size="10" type="text" value="293.61">
13      <label>Standard Deviation value</label>
14    </param>
15    <param name="minsd" size="10" type="text" value="2.5">
16      <label>Minimum SD</label>
17    </param>
18    <param name="eightyseven" type="select">
19      <label>Use the old (1987) weight data</label>
20      <option value="no">No</option>
21      <option value="yes">Yes</option>
22    </param>
23    <param name="out_format1" type="select">
24      <label>Output Report File Format</label>
25      <option value="motif">Motif</option>
26      <option value="embl">EMBL</option>
27      <option value="genbank">GENBANK</option>
28      <option value="gff">GFF</option>
29      <option value="pir">PIR</option>
30      <option value="swiss">SwissProt</option>
31      <option value="dbmotif">DbMotif</option>
32      <option value="diffseq">Diffseq</option>
33      <option value="excel">Excel (tab delimited)</option>
34      <option value="feattable">FeatTable</option>
35      <option value="regions">Regions</option>
36      <option value="seqtable">SeqTable</option>
37      <option value="simple">SRS Simple</option>
38      <option value="srs">SRS</option>
39      <option value="table">Table</option>
40      <option value="tagseq">TagSeq</option>
41    </param>
42  </inputs>
43  <outputs>
44    <data format="motif" name="out_file1" />
45  </outputs>
46  <tests>
47    <test>
48      <param name="input1" value="2.fasta"/>
49      <param name="mean" value="238.71"/>
50      <param name="sd" value="293.61"/>
51      <param name="minsd" value="2.5"/>
52      <param name="eightyseven" value="no"/>
53      <param name="out_format1" value="excel"/>
54      <output name="out_file1" file="emboss_helixturnhelix_out.tabular"/>
55    </test>
56  </tests>
57  <code file="emboss_format_corrector.py" />
58  <help>
59    You can view the original documentation here_.
60    
61    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.html
62
63------
64
65**Citation**
66
67If 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;`_
68  </help>
69</tool>