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