annotate emboss_palindrome.xml @ 14:2e0fb4bc860e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit fed02ef07e0a45f0d5a89cdca364607ab8da6cf9
author iuc
date Mon, 28 Jan 2019 11:22:18 -0500
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: palindrome65" name="palindrome" version="@VERSION@.1">
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2 <description>Looks for inverted repeats in a nucleotide sequence</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 <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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8 <inputs>
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9 <param name="input1" type="data" format="fasta" label="Sequences" />
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10 <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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11 <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" />
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="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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13 <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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14 <param name="overlap" type="select" label="Report overlapping matches">
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15 <option value="yes">Yes</option>
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16 <option value="no">No</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data name="out_file1" format="palindrome" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <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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25 <param name="minpallen" value="10"/>
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26 <param name="maxpallen" value="100"/>
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27 <param name="gaplimit" value="100"/>
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28 <param name="nummismatches" value="0"/>
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29 <param name="overlap" value="yes"/>
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30 <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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31 </test>
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32 </tests>
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33 <help>
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34 .. class:: warningmark
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35
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36 The input dataset needs to be sequences.
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37
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38 -----
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39
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40 You can view the original documentation here_.
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41
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42 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/palindrome.html
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43 </help>
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44 <expand macro="citations" />
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45 </tool>