/tools/emboss_5/emboss_pepwheel.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 51 lines · 46 code · 4 blank · 1 comment · 0 complexity · 6e49eb482c8222199f48e86de5d6e7a4 MD5 · raw file
- <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
- <!-- produces png file -->
- <description>Shows protein sequences as helices</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
- $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
- <inputs>
- <param format="data" name="input1" type="data">
- <label>Sequence</label>
- </param>
- <param name="steps" size="10" type="text" value="18">
- <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
- </param>
- <param name="turns" size="10" type="text" value="5">
- <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
- </param>
- <param name="squares" size="10" type="text" value="ILVM">
- <label>Residues to mark with squares</label>
- </param>
- <param name="diamonds" size="10" type="text" value="DENQST">
- <label>Residues to mark with diamonds</label>
- </param>
- <param name="octags" size="10" type="text" value="HKR">
- <label>Residues to mark with octagons</label>
- </param>
- <param name="wheel" type="select">
- <label>Plot the wheel</label>
- <option value="yes">Yes</option>
- <option value="no">No</option>
- </param>
- <param name="amphipathic" type="select">
- <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- </inputs>
- <outputs>
- <data format="png" name="out_file1" />
- </outputs>
- <help>
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.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>