/tools/emboss_5/emboss_dan.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 90 lines · 66 code · 4 blank · 20 comment · 0 complexity · 5aa0ef0dcac230aeca3b5a59919fda33 MD5 · raw file
- <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
- <description>Calculates DNA RNA/DNA melting temperature</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
- -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
- <inputs>
- <param format="data" name="input1" type="data">
- <label>On query</label>
- </param>
- <param name="window" size="4" type="text" value="20">
- <label>Window Size</label>
- </param>
- <param name="shift" size="4" type="text" value="1">
- <label>Step size (shift increment)</label>
- </param>
- <param name="dnaconc" size="4" type="text" value="50.0">
- <label>DNA Concentration (nM)</label>
- </param>
- <param name="saltconc" size="4" type="text" value="50.0">
- <label>Salt concentration (mM)</label>
- </param>
- <param name="thermo" type="select">
- <label>Output the DeltaG, DeltaH and DeltaS values</label>
- <option value="yes">Yes</option>
- <option value="no">No</option>
- </param>
- <param name="temperature" size="4" type="text" value="25 ">
- <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
- </param>
- <param name="rna" type="select">
- <label>Sequence is RNA</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- <param name="product" type="select">
- <label>Include percent formamide, percent of mismatches allowed and product length</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- <param name="formamide" size="4" type="text" value="0 ">
- <label>Formamide concentration (nM)</label>
- </param>
- <param name="mismatch" size="4" type="text" value="0 ">
- <label>Percent mismatch to be used in calculations</label>
- </param>
- <param name="prodlen" size="4" type="text" value="20">
- <label>Product length to be used in calculations</label>
- </param>
- <param name="plot1" type="select">
- <label>Create a graph</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- </inputs>
- <outputs>
- <data format="dan" name="out_file1" />
- </outputs>
- <!--
- <tests>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="window" value="20"/>
- <param name="shift" value="1"/>
- <param name="dnaconc" value="50"/>
- <param name="saltconc" value="50"/>
- <param name="thermo" value="yes"/>
- <param name="temperature" value="25"/>
- <param name="rna" value="no"/>
- <param name="product" value="no"/>
- <param name="formamide" value="0"/>
- <param name="mismatch" value="0"/>
- <param name="prodlen" value="20"/>
- <param name="plot1" value="yes"/>
- <output name="out_file1" file="emboss_dan_out.png"/>
- </test>
- </tests>
- -->
- <code file="emboss_format_corrector.py" />
- <help>
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html
-
- ------
-
- **Citation**
-
- If 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>