Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_pepnet.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0"> | |
| 2 <!-- graphical output file with path information --> | |
| 3 <description>Displays proteins as a helical net</description> | |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 5 <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>Sequence</label> | |
| 9 </param> | |
| 10 <param name="squares" size="10" type="text" value="ILVM"> | |
| 11 <label>Residues to mark with squares</label> | |
| 12 </param> | |
| 13 <param name="diamonds" size="10" type="text" value="DENQST"> | |
| 14 <label>Residues to mark with diamonds</label> | |
| 15 </param> | |
| 16 <param name="octags" size="10" type="text" value="HKR "> | |
| 17 <label>Residues to mark with octagons</label> | |
| 18 </param> | |
| 19 <param name="amphipathic" type="select"> | |
| 20 <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> | |
| 21 <option value="no">No</option> | |
| 22 <option value="yes">Yes</option> | |
| 23 </param> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="png" name="out_file1" /> | |
| 27 </outputs> | |
| 28 <help> | |
| 29 You can view the original documentation here_. | |
| 30 | |
| 31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepnet.html | |
| 32 </help> | |
| 33 </tool> |