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1 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
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2 <description>Count composition of dimer/trimer/etc words in a sequence</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>On query</label>
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8 </param>
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9 <param name="word" size="4" type="text" value="2">
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10 <label>Size of word (window) to count</label>
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11 </param>
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12 <param name="frame" type="select">
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13 <label>Frame to inspect</label>
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14 <option value="0">All Frames</option>
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15 <option value="1">Frame 1</option>
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16 <option value="2">Frame 2</option>
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17 <option value="3">Frame 3</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="compseq" name="out_file1" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input1" value="2.fasta"/>
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26 <param name="word" value="2"/>
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27 <param name="frame" value="0"/>
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28 <output name="out_file1" file="emboss_compseq_out.compseq"/>
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29 </test>
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30 </tests>
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31 <help>
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32 .. class:: warningmark
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33
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34 The input dataset needs to be sequences.
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35
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36 -----
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37
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38 You can view the original documentation here_.
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39
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40 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
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41 </help>
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42 </tool>
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