annotate emboss_sixpack.xml @ 17:ce385837c160 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"
author iuc
date Fri, 20 Nov 2020 16:51:11 +0000
parents 8992d258e42f
children
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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: sixpack90" name="sixpack" version="@VERSION@+galaxy2">
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2 <!-- tool adds file description and timestamp to output data -->
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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3 <description>Display a DNA sequence with 6-frame translation and ORFs</description>
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4 <macros>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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5 <import>macros.xml</import>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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6 </macros>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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7 <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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8 <code file="emboss_format_corrector.py" />
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9 <command><![CDATA[
8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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10 sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize
8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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11 #if str($uppercase):
8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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12 -uppercase '$uppercase'
8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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13 #end if
8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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14 -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto]]></command>
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15 <inputs>
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16 <param name="input1" type="data" format="fasta" label="Sequences" />
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17 <param name="table" type="select" label="Code to use">
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18 <option value="0">Standard</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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19 <option value="1">Standard (with alternative initiation codons)</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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20 <option value="2">Vertebrate Mitochondrial</option>
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21 <option value="3">Yeast Mitochondrial</option>
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22 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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23 <option value="5">Invertebrate Mitochondrial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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24 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
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25 <option value="9">Echinoderm Mitochondrial</option>
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26 <option value="10">Euplotid Nuclear</option>
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27 <option value="11">Bacterial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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28 <option value="12">Alternative Yeast Nuclear</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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29 <option value="13">Ascidian Mitochondrial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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30 <option value="14">Flatworm Mitochondrial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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31 <option value="15">Blepharisma Macronuclear</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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32 <option value="16">Chlorophycean Mitochondrial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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33 <option value="21">Trematode Mitochondrial</option>
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34 <option value="22">Scenedesmus obliquus</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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35 <option value="23">Thraustochytrium Mitochondrial</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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36 </param>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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37 <param name="firstorf" type="select" label="Count the beginning of a sequence as a possible ORF">
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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38 <option value="yes">Yes</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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39 <option value="no">No</option>
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40 </param>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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41 <param name="lastorf" type="select" label="Count the end of a sequence as a possible ORF">
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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42 <option value="yes">Yes</option>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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43 <option value="no">No</option>
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44 </param>
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45 <param name="mstart" type="select" label="Displays only ORFs starting with an M">
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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46 <option value="no">No</option>
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47 <option value="yes">Yes</option>
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48 </param>
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49 <param name="reverse" type="select" label="Display the translation of the DNA sequence in the 3 reverse frames">
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50 <option value="yes">Yes</option>
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51 <option value="no">No</option>
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52 </param>
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53 <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
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54 <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/>
10
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55 <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
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56 <option value="yes">Yes</option>
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57 <option value="no">No</option>
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58 </param>
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59 <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />
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60 <param name="length" type="integer" value="0" label="Line length of page" />
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61 <param name="margin" type="integer" value="10" label="Margin around sequence for numbering" />
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62 <param name="disp_name" type="select" label="Display the ID name of the sequence">
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63 <option value="yes">Yes</option>
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64 <option value="no">No</option>
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65 </param>
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66 <param name="description" type="select" label="Display the description of the sequence">
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67 <option value="yes">Yes</option>
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68 <option value="no">No</option>
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69 </param>
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70 <param name="offset" type="integer" value="1" label="Number from which you want the DNA sequence to be numbered" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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71 <param name="html_out1" type="select" label="Format output as an HTML table">
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72 <option value="no">No</option>
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73 <option value="yes">Yes</option>
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74 </param>
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75 <param name="out_format2" type="select" label="Output sequence file format">
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76 <option value="fasta">FASTA (m)</option>
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77 <option value="acedb">ACeDB (m)</option>
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78 <option value="asn1">ASN.1 (m)</option>
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79 <option value="clustal">Clustal (m)</option>
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80 <option value="codata">CODATA (m)</option>
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81 <option value="embl">EMBL (m)</option>
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82 <option value="fitch">Fitch (m)</option>
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83 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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84 <option value="genbank">GENBANK (m)</option>
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85 <option value="gff">GFF (m)</option>
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86 <option value="hennig86">Hennig86 (m)</option>
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87 <option value="ig">Intelligenetics (m)</option>
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88 <option value="jackknifer">Jackknifer (m)</option>
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89 <option value="jackknifernon">Jackknifernon (m)</option>
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90 <option value="mega">Mega (m)</option>
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91 <option value="meganon">Meganon (m)</option>
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92 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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93 <option value="pir">NBRF (PIR) (m)</option>
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94 <option value="ncbi">NCBI style FASTA (m)</option>
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95 <option value="nexus">Nexus/PAUP (m)</option>
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96 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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97 <option value="phylip">PHYLIP interleaved (m)</option>
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98 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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99 <option value="selex">SELEX (m)</option>
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100 <option value="staden">Staden (s)</option>
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101 <option value="strider">DNA strider (m)</option>
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102 <option value="swiss">SwisProt entry (m)</option>
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103 <option value="text">Plain sequence (s)</option>
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104 <option value="treecon">Treecon (m)</option>
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105 </param>
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106 </inputs>
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107 <outputs>
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108 <data name="ofile1" format="sixpack" />
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109 <data name="ofile2" format="fasta" />
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110 </outputs>
13
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111 <tests>
10
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112 <test>
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113 <param name="input1" value="2.fasta"/>
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114 <param name="table" value="0"/>
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115 <param name="firstorf" value="no"/>
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116 <param name="lastorf" value="no"/>
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117 <param name="mstart" value="no"/>
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118 <param name="reverse" value="no"/>
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119 <param name="orfminsize" value="1"/>
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120 <param name="uppercase" value=""/>
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121 <param name="number" value="no"/>
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122 <param name="width" value="60"/>
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123 <param name="length" value="0"/>
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124 <param name="margin" value="10"/>
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125 <param name="disp_name" value="no"/>
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126 <param name="description" value="no"/>
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127 <param name="offset" value="1"/>
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128 <param name="html_out1" value="no"/>
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129 <param name="out_format2" value="fasta"/>
13
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130 <output name="ofile1" file="emboss_sixpack_out2.sixpack" />
10
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131 <output name="ofile2" file="emboss_sixpack_out.fasta"/>
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132 </test>
13
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133 </tests>
10
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134 <help>
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135 .. class:: warningmark
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136
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137 The input dataset needs to be sequences.
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138
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139 -----
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140
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141 You can view the original documentation here_.
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142
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143 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html
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144 </help>
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145 <expand macro="citations" />
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146 </tool>