root/galaxy-central/tools/emboss_5/emboss_pepnet.xml @ 3

リビジョン 2, 1.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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>
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