[2] | 1 | <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
|
---|
| 2 | <description>Calculates DNA RNA/DNA melting temperature</description>
|
---|
| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
---|
| 4 | <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
|
---|
| 5 | -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
|
---|
| 6 | <inputs>
|
---|
| 7 | <param format="data" name="input1" type="data">
|
---|
| 8 | <label>On query</label>
|
---|
| 9 | </param>
|
---|
| 10 | <param name="window" size="4" type="text" value="20">
|
---|
| 11 | <label>Window Size</label>
|
---|
| 12 | </param>
|
---|
| 13 | <param name="shift" size="4" type="text" value="1">
|
---|
| 14 | <label>Step size (shift increment)</label>
|
---|
| 15 | </param>
|
---|
| 16 | <param name="dnaconc" size="4" type="text" value="50.0">
|
---|
| 17 | <label>DNA Concentration (nM)</label>
|
---|
| 18 | </param>
|
---|
| 19 | <param name="saltconc" size="4" type="text" value="50.0">
|
---|
| 20 | <label>Salt concentration (mM)</label>
|
---|
| 21 | </param>
|
---|
| 22 | <param name="thermo" type="select">
|
---|
| 23 | <label>Output the DeltaG, DeltaH and DeltaS values</label>
|
---|
| 24 | <option value="yes">Yes</option>
|
---|
| 25 | <option value="no">No</option>
|
---|
| 26 | </param>
|
---|
| 27 | <param name="temperature" size="4" type="text" value="25 ">
|
---|
| 28 | <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
|
---|
| 29 | </param>
|
---|
| 30 | <param name="rna" type="select">
|
---|
| 31 | <label>Sequence is RNA</label>
|
---|
| 32 | <option value="no">No</option>
|
---|
| 33 | <option value="yes">Yes</option>
|
---|
| 34 | </param>
|
---|
| 35 | <param name="product" type="select">
|
---|
| 36 | <label>Include percent formamide, percent of mismatches allowed and product length</label>
|
---|
| 37 | <option value="no">No</option>
|
---|
| 38 | <option value="yes">Yes</option>
|
---|
| 39 | </param>
|
---|
| 40 | <param name="formamide" size="4" type="text" value="0 ">
|
---|
| 41 | <label>Formamide concentration (nM)</label>
|
---|
| 42 | </param>
|
---|
| 43 | <param name="mismatch" size="4" type="text" value="0 ">
|
---|
| 44 | <label>Percent mismatch to be used in calculations</label>
|
---|
| 45 | </param>
|
---|
| 46 | <param name="prodlen" size="4" type="text" value="20">
|
---|
| 47 | <label>Product length to be used in calculations</label>
|
---|
| 48 | </param>
|
---|
| 49 | <param name="plot1" type="select">
|
---|
| 50 | <label>Create a graph</label>
|
---|
| 51 | <option value="no">No</option>
|
---|
| 52 | <option value="yes">Yes</option>
|
---|
| 53 | </param>
|
---|
| 54 | </inputs>
|
---|
| 55 | <outputs>
|
---|
| 56 | <data format="dan" name="out_file1" />
|
---|
| 57 | </outputs>
|
---|
| 58 | <!-- |
---|
| 59 | <tests> |
---|
| 60 | <test> |
---|
| 61 | <param name="input1" value="2.fasta"/> |
---|
| 62 | <param name="window" value="20"/> |
---|
| 63 | <param name="shift" value="1"/> |
---|
| 64 | <param name="dnaconc" value="50"/> |
---|
| 65 | <param name="saltconc" value="50"/> |
---|
| 66 | <param name="thermo" value="yes"/> |
---|
| 67 | <param name="temperature" value="25"/> |
---|
| 68 | <param name="rna" value="no"/> |
---|
| 69 | <param name="product" value="no"/> |
---|
| 70 | <param name="formamide" value="0"/> |
---|
| 71 | <param name="mismatch" value="0"/> |
---|
| 72 | <param name="prodlen" value="20"/> |
---|
| 73 | <param name="plot1" value="yes"/> |
---|
| 74 | <output name="out_file1" file="emboss_dan_out.png"/> |
---|
| 75 | </test> |
---|
| 76 | </tests>
|
---|
| 77 | -->
|
---|
| 78 | <code file="emboss_format_corrector.py" />
|
---|
| 79 | <help> |
---|
| 80 | You can view the original documentation here_. |
---|
| 81 | |
---|
| 82 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html |
---|
| 83 | </help> |
---|
| 84 | </tool> |
---|