Mercurial > repos > devteam > emboss_5

annotate emboss_getorf.xml @ 16:33381b9c268c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522
author iuc
date Mon, 28 Jan 2019 14:49:47 -0500
parents 27c43fb015f0
children 21a9fb508031
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27c43fb015f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
parents: 11
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1 <tool id="EMBOSS: getorf42" name="getorf" version="@VERSION@.1">
11
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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2 <description>Finds and extracts open reading frames (ORFs)</description>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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3 <macros>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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4 <import>macros.xml</import>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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5 </macros>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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6 <expand macro="requirements" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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7 <code file="emboss_format_corrector.py" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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8 <command>getorf -sequence '$input1' -outseq '$out_file1' -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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9 -osformat2 $out_format1 -auto</command>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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10 <inputs>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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11 <param name="input1" type="data" format="fasta" label="Sequences" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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12 <param name="table" type="select" label="Code to use">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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13 <option value="0">Standard</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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14 <option value="1">Standard (with alternative initiation codons)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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15 <option value="2">Vertebrate Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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16 <option value="3">Yeast Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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18 <option value="5">Invertebrate Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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19 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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20 <option value="9">Echinoderm Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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21 <option value="10">Euplotid Nuclear</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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22 <option value="11">Bacterial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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23 <option value="12">Alternative Yeast Nuclear</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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24 <option value="13">Ascidian Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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25 <option value="14">Flatworm Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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26 <option value="15">Blepharisma Macronuclear</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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27 <option value="16">Chlorophycean Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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28 <option value="21">Trematode Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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29 <option value="22">Scenedesmus obliquus</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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30 <option value="23">Thraustochytrium Mitochondrial</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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31 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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32 <param name="minsize" type="integer" value="30" label="Minimum nucleotide size of ORF to report" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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33 <param name="maxsize" type="integer" value="1000000" label="Maximum nucleotide size of ORF to report" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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34 <param name="find" type="select" label="What to output">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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35 <option value="0">Translation of regions between STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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36 <option value="1">Translation of regions between START and STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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37 <option value="2">Nucleic sequences between STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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38 <option value="3">Nucleic sequences between START and STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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39 <option value="4">Nucleotides flanking START codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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40 <option value="5">Nucleotides flanking initial STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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41 <option value="6">Nucleotides flanking ending STOP codons</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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42 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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43 <param name="methionine" type="select" label="All START codons to code for Methionine">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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44 <option value="yes">Yes</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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45 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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46 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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47 <param name="circular" type="select" label="Circular sequence">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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48 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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49 <option value="yes">Yes</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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50 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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51 <param name="reverse" type="select" label="Find ORFs in the reverse complement">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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52 <option value="yes">Yes</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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53 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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54 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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55 <param name="flanking" type="integer" value="100" label="Number of flanking nucleotides to output" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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56 <param name="out_format1" type="select" label="Output sequence file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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57 <option value="fasta">FASTA (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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58 <option value="acedb">ACeDB (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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59 <option value="asn1">ASN.1 (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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60 <option value="clustal">Clustal (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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61 <option value="codata">CODATA (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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62 <option value="embl">EMBL (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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63 <option value="fitch">Fitch (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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64 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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65 <option value="genbank">GENBANK (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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66 <!-- <option value="gff">GFF (m)</option> -->
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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67 <option value="hennig86">Hennig86 (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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68 <option value="ig">Intelligenetics (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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69 <option value="jackknifer">Jackknifer (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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70 <option value="jackknifernon">Jackknifernon (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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71 <option value="mega">Mega (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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72 <option value="meganon">Meganon (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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73 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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74 <option value="pir">NBRF (PIR) (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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75 <option value="ncbi">NCBI style FASTA (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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76 <option value="nexus">Nexus/PAUP (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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77 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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78 <option value="phylip">PHYLIP interleaved (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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79 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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80 <option value="selex">SELEX (m)</option>
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81 <option value="staden">Staden (s)</option>
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82 <option value="strider">DNA strider (m)</option>
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83 <option value="swiss">SwisProt entry (m)</option>
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84 <option value="text">Plain sequence (s)</option>
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85 <option value="treecon">Treecon (m)</option>
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86 </param>
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87 </inputs>
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88 <outputs>
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89 <data name="out_file1" format="fasta" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input1" value="2.fasta"/>
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94 <param name="minsize" value="30"/>
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95 <param name="maxsize" value="1000000"/>
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96 <param name="find" value="0"/>
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97 <param name="methionine" value="yes"/>
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98 <param name="circular" value="no"/>
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99 <param name="reverse" value="yes"/>
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100 <param name="table" value="0"/>
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101 <param name="flanking" value="100"/>
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102 <param name="out_format1" value="fasta"/>
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103 <output name="out_file1" file="emboss_getorf_out.fasta"/>
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104 </test>
11
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105 </tests>
10
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106 <help>
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107 .. class:: warningmark
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108
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109 The input dataset needs to be sequences.
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110
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111 -----
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112
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113 You can view the original documentation here_.
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114
11
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115 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/getorf.html
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116 </help>
11
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117 <expand macro="citations" />
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118 </tool>