annotate emboss_antigenic.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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10
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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1 <tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0.1">
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2 <description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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7 <code file="emboss_format_corrector.py" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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8 <command>antigenic -sequence '$input1' -outfile '$out_file1' -minlen $minlen -rformat2 $out_format1 -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="data" label="On query" />
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11 <param name="minlen" type="integer" value="6" label="Minimum length of region" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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12 <param name="out_format1" type="select" label="Output format">
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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13 <option value="gff">GFF</option>
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14 <option value="pir">PIR</option>
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15 <option value="swiss">SwissProt</option>
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16 <option value="dbmotif">DbMotif</option>
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17 <option value="diffseq">diffseq</option>
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18 <option value="excel">Excel (TAB Delimited)</option>
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19 <option value="feattable">FeatTable</option>
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20 <option value="motif">Motif</option>
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21 <option value="nametable">NameTable</option>
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22 <option value="regions">Regions</option>
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23 <option value="seqtable">SeqTable</option>
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24 <option value="simple">SRS simple</option>
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25 <option value="srs">SRS</option>
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26 <option value="table">Table</option>
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27 <option value="tagseq">Tagseq</option>
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28 <option value="antigenic">Antigenic Output File</option>
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29 </param>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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30 </inputs>
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31 <outputs>
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32 <data name="out_file1" format="antigenic" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input1" value="2.fasta"/>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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37 <param name="minlen" value="6"/>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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38 <param name="out_format1" value="excel"/>
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39 <output name="out_file1" file="emboss_antigenic_out.tabular"/>
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40 </test>
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41 </tests>
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42 <help>
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43 You can view the original documentation here_.
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44
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45 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/antigenic.html
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46 </help>
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47 <expand macro="citations" />
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48 </tool>