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annotate emboss_compseq.xml @ 20:21a9fb508031 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:05:39 +0000
parents 27c43fb015f0
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27c43fb015f0 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: compseq14" name="compseq" version="@VERSION@.1">
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2 <description>Count composition of dimer/trimer/etc words in a sequence</description>
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21a9fb508031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>compseq -sequence '$input1' -outfile '$out_file1' -word $word -frame $frame -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="On query" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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11 <param name="word" type="integer" value="2" label="Size of word (window) to count" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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12 <param name="frame" type="select" label="Frame to inspect">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <option value="0">All Frames</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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14 <option value="1">Frame 1</option>
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15 <option value="2">Frame 2</option>
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16 <option value="3">Frame 3</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="compseq" />
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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"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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25 <param name="word" value="2"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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26 <param name="frame" value="0"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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27 <output name="out_file1" file="emboss_compseq_out.compseq"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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28 </test>
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29 </tests>
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30 <help>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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31 .. class:: warningmark
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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33 The input dataset needs to be sequences.
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35 -----
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37 You can view the original documentation here_.
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38
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39 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/compseq.html
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40 </help>
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41 <expand macro="citations" />
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42 </tool>