Mercurial > repos > devteam > emboss_5
diff emboss_pepwheel.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_pepwheel.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepwheel.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,53 +1,35 @@ -<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0"> +<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0.1"> <!-- 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 $wheel -auto</command> - <inputs> - <param format="data" name="input1" type="data"> - <label>Sequence</label> - </param> - <param name="steps" type="text" value="18"> - <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label> - </param> - <param name="turns" type="text" value="5"> - <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label> - </param> - <param name="squares" type="text" value="ILVM"> - <label>Residues to mark with squares</label> - </param> - <param name="diamonds" type="text" value="DENQST"> - <label>Residues to mark with diamonds</label> - </param> - <param name="octags" type="text" value="HKR"> - <label>Residues to mark with octagons</label> - </param> - <param name="wheel" type="select"> - <label>Plot the wheel</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="amphipathic" type="select"> - <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - </inputs> - <outputs> - <data format="png" name="out_file1" /> - </outputs> + <description>Shows protein sequences as helices</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>perl '$__tool_directory__/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 name="input1" type="data" format="data" label="Sequence" /> + <param name="steps" type="integer" value="18" label="Steps, the number of residues plotted per turn is this value divided by the 'turns' value" /> + <param name="turns" type="integer" value="5" label="Turns, the number of residues plotted per turn is the 'steps' value divided by this value" /> + <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" /> + <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" /> + <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" /> + <param name="wheel" type="select" label="Plot the wheel"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="amphipathic" type="select" label="Amphipathic?" help="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" > + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="png" /> + </outputs> <help> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -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>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwheel.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>