Mercurial > repos > devteam > emboss_5
annotate emboss_diffseq.xml @ 20:21a9fb508031 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
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| date | Tue, 31 Aug 2021 08:05:39 +0000 |
| parents | 27c43fb015f0 |
| children |
| rev | line source |
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27c43fb015f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
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1 <tool id="EMBOSS: diffseq22" name="diffseq" version="@VERSION@.1"> |
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11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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2 <description>Find differences between nearly identical sequences</description> |
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21a9fb508031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <expand macro="bio_tools" /> |
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11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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4 <macros> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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5 <import>macros.xml</import> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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6 </macros> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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7 <expand macro="requirements" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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8 <code file="emboss_format_corrector.py" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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9 <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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10 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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11 <inputs> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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12 <param name="input1" type="data" format="data" label="Sequence 1" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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13 <param name="input2" type="data" format="data" label="Sequence 2" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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14 <param name="wordsize" type="integer" value="20" label="Wordsize" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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15 <param name="globaldifferences" type="select" label="Report differences at the ends"> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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16 <option value="no">No</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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17 <option value="yes">Yes</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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18 </param> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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19 <param name="out_format1" type="select" label="Output report file format"> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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20 <option value="diffseq">Diffseq</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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21 <option value="embl">EMBL</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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22 <option value="genbank">GENBANK</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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23 <option value="gff">GFF</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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24 <option value="pir">PIR</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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25 <option value="swiss">SwissProt</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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26 <option value="dbmotif">DbMotif</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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27 <option value="excel">Excel (tab delimited)</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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28 <option value="feattable">FeatTable</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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29 <option value="motif">Motif</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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30 <option value="regions">Regions</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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31 <option value="seqtable">SeqTable</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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32 <option value="simple">SRS Simple</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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33 <option value="srs">SRS</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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34 <option value="table">Table</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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35 <option value="tagseq">TagSeq</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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36 </param> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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37 <param name="out_format2" type="select" label="Sequence 1 output feature file format"> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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38 <option value="gff">GFF</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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39 <option value="embl">EMBL</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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40 <option value="swiss">SwissProt</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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41 </param> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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42 <param name="out_format3" type="select" label="Sequence 2 output feature file format"> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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43 <option value="gff">GFF</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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44 <option value="embl">EMBL</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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45 <option value="swiss">SwissProt</option> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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46 </param> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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47 </inputs> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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48 <outputs> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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49 <data name="out_file1" format="diffseq" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
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50 <data name="out_file2" format="gff" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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51 <data name="out_file3" format="gff" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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52 </outputs> |
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9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
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53 <help> |
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9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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54 You can view the original documentation here_. |
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9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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55 |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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56 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/diffseq.html |
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9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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57 </help> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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58 <expand macro="citations" /> |
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0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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59 </tool> |