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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> |
