[2] | 1 | <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
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| 2 | <!-- tool adds file description and timestamp to output data --> |
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| 3 | <description>Display a DNA sequence with 6-frame translation and ORFs</description>
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| 4 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 5 | <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
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| 6 | "$uppercase" -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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| 7 | <inputs>
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| 8 | <param format="fasta" name="input1" type="data">
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| 9 | <label>Sequences</label>
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| 10 | </param>
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| 11 | <param name="table" type="select">
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| 12 | <label>Code to use</label>
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| 13 | <option value="0">Standard</option>
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| 14 | <option value="1">Standard (with alternative initiation codons)</option>
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| 15 | <option value="2">Vertebrate Mitochondrial</option>
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| 16 | <option value="3">Yeast Mitochondrial</option>
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| 17 | <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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| 18 | <option value="5">Invertebrate Mitochondrial</option>
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| 19 | <option value="6">Ciliate Macronuclear and Dasycladacean</option>
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| 20 | <option value="9">Echinoderm Mitochondrial</option>
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| 21 | <option value="10">Euplotid Nuclear</option>
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| 22 | <option value="11">Bacterial</option>
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| 23 | <option value="12">Alternative Yeast Nuclear</option>
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| 24 | <option value="13">Ascidian Mitochondrial</option>
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| 25 | <option value="14">Flatworm Mitochondrial</option>
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| 26 | <option value="15">Blepharisma Macronuclear</option>
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| 27 | <option value="16">Chlorophycean Mitochondrial</option>
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| 28 | <option value="21">Trematode Mitochondrial</option>
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| 29 | <option value="22">Scenedesmus obliquus</option>
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| 30 | <option value="23">Thraustochytrium Mitochondrial</option>
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| 31 | </param>
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| 32 | <param name="firstorf" type="select">
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| 33 | <label>Count the beginning of a sequence as a possible ORF</label>
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| 34 | <option value="yes">Yes</option>
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| 35 | <option value="no">No</option>
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| 36 | </param>
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| 37 | <param name="lastorf" type="select">
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| 38 | <label>Count the end of a sequence as a possible ORF</label>
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| 39 | <option value="yes">Yes</option>
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| 40 | <option value="no">No</option>
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| 41 | </param>
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| 42 | <param name="mstart" type="select">
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| 43 | <label>Displays only ORFs starting with an M</label>
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| 44 | <option value="no">No</option>
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| 45 | <option value="yes">Yes</option>
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| 46 | </param>
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| 47 | <param name="reverse" type="select">
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| 48 | <label>Display the translation of the DNA sequence in the 3 reverse frames</label>
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| 49 | <option value="yes">Yes</option>
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| 50 | <option value="no">No</option>
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| 51 | </param>
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| 52 | <param name="orfminsize" size="4" type="text" value="1">
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| 53 | <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label>
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| 54 | </param>
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| 55 | <param name="uppercase" size="50" type="text" value="">
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| 56 | <label>Regions to put in uppercase</label>
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| 57 | </param>
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| 58 | <param name="number" type="select">
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| 59 | <label>Number the sequence at the beginning and the end of each line</label>
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| 60 | <option value="yes">Yes</option>
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| 61 | <option value="no">No</option>
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| 62 | </param>
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| 63 | <param name="width" size="4" type="text" value="60">
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| 64 | <label>Number of nucleotides displayed on each line</label>
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| 65 | </param>
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| 66 | <param name="length" size="4" type="text" value="0">
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| 67 | <label>Line length of page</label>
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| 68 | </param>
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| 69 | <param name="margin" size="4" type="text" value="10">
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| 70 | <label>Margin around sequence for numbering</label>
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| 71 | </param>
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| 72 | <param name="disp_name" type="select">
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| 73 | <label>Display the ID name of the sequence</label>
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| 74 | <option value="yes">Yes</option>
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| 75 | <option value="no">No</option>
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| 76 | </param>
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| 77 | <param name="description" type="select">
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| 78 | <label>Display the description of the sequence</label>
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| 79 | <option value="yes">Yes</option>
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| 80 | <option value="no">No</option>
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| 81 | </param>
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| 82 | <param name="offset" size="4" type="text" value="1">
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| 83 | <label>Number from which you want the DNA sequence to be numbered</label>
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| 84 | </param>
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| 85 | <param name="html_out1" type="select">
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| 86 | <label>Format output as an HTML table</label>
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| 87 | <option value="no">No</option>
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| 88 | <option value="yes">Yes</option>
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| 89 | </param>
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| 90 | <param name="out_format2" type="select">
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| 91 | <label>Output Sequence File Format</label>
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| 92 | <option value="fasta">FASTA (m)</option>
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| 93 | <option value="acedb">ACeDB (m)</option>
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| 94 | <option value="asn1">ASN.1 (m)</option>
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| 95 | <option value="clustal">Clustal (m)</option>
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| 96 | <option value="codata">CODATA (m)</option>
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| 97 | <option value="embl">EMBL (m)</option>
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| 98 | <option value="fitch">Fitch (m)</option>
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| 99 | <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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| 100 | <option value="genbank">GENBANK (m)</option>
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| 101 | <option value="gff">GFF (m)</option>
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| 102 | <option value="hennig86">Hennig86 (m)</option>
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| 103 | <option value="ig">Intelligenetics (m)</option>
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| 104 | <option value="jackknifer">Jackknifer (m)</option>
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| 105 | <option value="jackknifernon">Jackknifernon (m)</option>
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| 106 | <option value="mega">Mega (m)</option>
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| 107 | <option value="meganon">Meganon (m)</option>
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| 108 | <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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| 109 | <option value="pir">NBRF (PIR) (m)</option>
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| 110 | <option value="ncbi">NCBI style FASTA (m)</option>
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| 111 | <option value="nexus">Nexus/PAUP (m)</option>
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| 112 | <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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| 113 | <option value="phylip">PHYLIP interleaved (m)</option>
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| 114 | <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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| 115 | <option value="selex">SELEX (m)</option>
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| 116 | <option value="staden">Staden (s)</option>
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| 117 | <option value="strider">DNA strider (m)</option>
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| 118 | <option value="swiss">SwisProt entry (m)</option>
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| 119 | <option value="text">Plain sequence (s)</option>
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| 120 | <option value="treecon">Treecon (m)</option>
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| 121 | </param>
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| 122 | </inputs>
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| 123 | <outputs>
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| 124 | <data format="sixpack" name="ofile1" />
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| 125 | <data format="fasta" name="ofile2" />
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| 126 | </outputs> |
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| 127 | <!-- <tests> |
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| 128 | <test> |
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| 129 | <param name="input1" value="2.fasta"/> |
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| 130 | <param name="table" value="0"/> |
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| 131 | <param name="firstorf" value="no"/> |
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| 132 | <param name="lastorf" value="no"/> |
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| 133 | <param name="mstart" value="no"/> |
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| 134 | <param name="reverse" value="no"/> |
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| 135 | <param name="orfminsize" value="1"/> |
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| 136 | <param name="uppercase" value=""/> |
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| 137 | <param name="number" value="no"/> |
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| 138 | <param name="width" value="60"/> |
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| 139 | <param name="length" value="0"/> |
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| 140 | <param name="margin" value="10"/> |
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| 141 | <param name="disp_name" value="no"/> |
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| 142 | <param name="description" value="no"/> |
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| 143 | <param name="offset" value="1"/> |
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| 144 | <param name="html_out1" value="no"/> |
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| 145 | <param name="out_format2" value="fasta"/> |
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| 146 | <output name="ofile2" file="emboss_sixpack_out.fasta"/> |
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| 147 | </test> |
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| 148 | </tests> -->
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| 149 | <code file="emboss_format_corrector.py" />
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| 150 | <help> |
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| 151 | |
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| 152 | .. class:: warningmark |
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| 153 | |
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| 154 | The input dataset needs to be sequences. |
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| 155 | |
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| 156 | ----- |
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| 157 | |
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| 158 | You can view the original documentation here_. |
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| 159 | |
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| 160 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html |
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| 161 | </help> |
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| 162 | </tool> |
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