Mercurial > repos > devteam > emboss_5

annotate emboss_tranalign.xml @ 15:dbd24c72f166 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit fed02ef07e0a45f0d5a89cdca364607ab8da6cf9
author iuc
date Mon, 28 Jan 2019 11:20:53 -0500
parents 27c43fb015f0
children 21a9fb508031
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14
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: tranalign100" name="tranalign" version="@VERSION@">
13
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
parents: 11
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2 <description>Align nucleic coding regions given the aligned proteins</description>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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3 <macros>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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4 <import>macros.xml</import>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
parents: 11
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5 </macros>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
parents: 11
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6 <expand macro="requirements" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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7 <code file="emboss_format_corrector.py" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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8 <command detect_errors="aggressive"><![CDATA[
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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9 tranalign
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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10 -asequence '$input1'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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11 -bsequence '$input2'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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12 -outseq '$out_file1'
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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13 -table $table
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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14 -osformat3 $out_format1
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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15 -auto
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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16 ]]></command>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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17 <inputs>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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18 <param name="input1" argument="-asequence" type="data" format="fasta" label="Nucleic sequences" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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19 <param name="input2" argument="-bsequence" type="data" format="data" label="Protein sequences" />
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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20 <param argument="-table" type="select" label="Code to use">
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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21 <option value="0">Standard</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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22 <option value="1">Standard (with alternative initiation codons)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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23 <option value="2">Vertebrate Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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24 <option value="3">Yeast Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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25 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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26 <option value="5">Invertebrate Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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27 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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28 <option value="9">Echinoderm Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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29 <option value="10">Euplotid Nuclear</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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30 <option value="11">Bacterial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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31 <option value="12">Alternative Yeast Nuclear</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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32 <option value="13">Ascidian Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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33 <option value="14">Flatworm Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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34 <option value="15">Blepharisma Macronuclear</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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35 <option value="16">Chlorophycean Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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36 <option value="21">Trematode Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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37 <option value="22">Scenedesmus obliquus</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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38 <option value="23">Thraustochytrium Mitochondrial</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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39 </param>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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40 <param name="out_format1" argument="-osformat3" type="select" label="Output sequence file format">
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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41 <option value="fasta">FASTA (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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42 <option value="acedb">ACeDB (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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43 <option value="asn1">ASN.1 (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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44 <option value="clustal">Clustal (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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45 <option value="codata">CODATA (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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46 <option value="embl">EMBL (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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47 <option value="fitch">Fitch (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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48 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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49 <option value="genbank">GENBANK (m)</option>
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50 <option value="gff">GFF (m)</option>
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51 <option value="hennig86">Hennig86 (m)</option>
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52 <option value="ig">Intelligenetics (m)</option>
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53 <option value="jackknifer">Jackknifer (m)</option>
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54 <option value="jackknifernon">Jackknifernon (m)</option>
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iuc
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55 <option value="mega">Mega (m)</option>
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56 <option value="meganon">Meganon (m)</option>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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57 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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58 <option value="pir">NBRF (PIR) (m)</option>
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59 <option value="ncbi">NCBI style FASTA (m)</option>
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60 <option value="nexus">Nexus/PAUP (m)</option>
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61 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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62 <option value="phylip">PHYLIP interleaved (m)</option>
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63 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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64 <option value="selex">SELEX (m)</option>
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65 <option value="staden">Staden (s)</option>
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66 <option value="strider">DNA strider (m)</option>
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67 <option value="swiss">SwisProt entry (m)</option>
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68 <option value="text">Plain sequence (s)</option>
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69 <option value="treecon">Treecon (m)</option>
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70 </param>
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71 </inputs>
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72 <outputs>
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73 <data name="out_file1" format="fasta" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="input1" value="3.fasta"/>
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78 <param name="input2" value="2.pep"/>
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79 <param name="table" value="0"/>
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80 <param name="out_format1" value="fasta"/>
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81 <output name="out_file1" file="emboss_tranalign_out.fasta"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 You can view the original documentation here_.
10
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86
13
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
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87 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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88 ]]></help>
d5c3794bd246 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
iuc
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89 <expand macro="citations" />
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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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90 </tool>