/tools/emboss_5/emboss_einverted.xml
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1<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0"> 2 <description>Finds DNA inverted repeats</description> 3 <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command> 4 <inputs> 5 <param format="fasta" name="input1" type="data"> 6 <label>On query</label> 7 </param> 8 <param name="gap" size="4" type="text" value="12"> 9 <label>Gap penalty</label> 10 </param> 11 <param name="threshold" size="4" type="text" value="50"> 12 <label>Minimum score threshold</label> 13 </param> 14 <param name="match" size="4" type="text" value="3"> 15 <label>Match score</label> 16 </param> 17 <param name="mismatch" size="4" type="text" value="-4"> 18 <label>Mismatch score</label> 19 </param> 20 <param name="maxrepeat" size="4" type="text" value="2000"> 21 <label>Maximum separation between the start of repeat and the end of the inverted repeat</label> 22 </param> 23 </inputs> 24 <outputs> 25 <data format="einverted" name="out_file1" /> 26 </outputs> 27 <tests> 28 <test> 29 <param name="input1" value="1.fasta"/> 30 <param name="gap" value="12"/> 31 <param name="threshold" value="50"/> 32 <param name="match" value="3"/> 33 <param name="mismatch" value="-4"/> 34 <param name="maxrepeat" value="2000"/> 35 <output name="out_file1" file="emboss_einverted_out.einverted"/> 36 </test> 37 </tests> 38 <help> 39.. class:: warningmark 40 41The input dataset needs to be sequences. 42 43----- 44 45 You can view the original documentation here_. 46 47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html 48 </help> 49</tool>