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annotate emboss_sixpack.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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" 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" 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" 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" 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" 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" 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
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162 ------
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163
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164 **Citation**
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165
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166 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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167
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168 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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169 </help>
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170 </tool>