/tools/emboss_5/emboss_helixturnhelix.xml
XML | 62 lines | 61 code | 1 blank | 0 comment | 0 complexity | 82fdb646a94f0d26cf25de2411cb4b60 MD5 | raw file
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>