Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_helixturnhelix.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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 </help> | |
| 63 </tool> |