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annotate emboss_est2genome.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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1 <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
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2 <description>Align EST and genomic DNA sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
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5 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
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6 <inputs>
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7 <param format="fasta" name="input1" type="data">
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8 <label>EST sequence(s)</label>
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9 </param>
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10 <param format="data" name="input2" type="data">
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11 <label>Genomic sequence</label>
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12 </param>
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13 <param name="match" type="text" value="1">
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14 <label>Score for matching two bases</label>
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15 </param>
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16 <param name="mismatch" type="text" value="1">
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17 <label>Cost for mismatching two bases</label>
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18 </param>
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19 <param name="gappenalty" type="text" value="2">
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20 <label>Cost for deleting a single base in either sequence, excluding introns</label>
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21 </param>
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22 <param name="intronpenalty" type="text" value="40">
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23 <label>Cost for an intron, independent of length</label>
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24 </param>
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25 <param name="splicepenalty" type="text" value="20">
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26 <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
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27 </param>
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28 <param name="minscore" type="text" value="30">
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29 <label>Exclude alignments with scores below this threshold score</label>
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30 </param>
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31 <param name="reverse" type="select">
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32 <label>Reverse the orientation of the EST sequence</label>
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33 <option value="no">No</option>
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34 <option value="yes">Yes</option>
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35 </param>
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36 <param name="splice" type="select">
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37 <label>Use donor and acceptor splice sites</label>
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38 <option value="yes">Yes</option>
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39 <option value="no">No</option>
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40 </param>
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41 <param name="mode" type="select">
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42 <label>Comparison mode</label>
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43 <option value="both">Both strands</option>
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44 <option value="forward">Forward strand only</option>
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45 <option value="reverse">Reverse strand only</option>
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46 </param>
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47 <param name="best" type="select">
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48 <label>Only best comparisons</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="shuffle" type="text" value="0">
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53 <label>Shuffle</label>
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54 </param>
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55 <param name="seed" type="text" value="20825">
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56 <label>Random number seed</label>
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57 </param>
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58 <param name="align" type="select">
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59 <label>Show the alignment</label>
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60 <option value="no">No</option>
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61 <option value="yes">Yes</option>
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62 </param>
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63 <param name="width" type="text" value="50">
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64 <label>Alignment width</label>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data format="est2genome" name="out_file1" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input1" value="2.fasta"/>
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73 <param name="input2" value="1.fasta"/>
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74 <param name="match" value="1"/>
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75 <param name="mismatch" value="1"/>
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76 <param name="match" value="1"/>
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77 <param name="gappenalty" value="2"/>
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78 <param name="intronpenalty" value="40"/>
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79 <param name="splicepenalty" value="20"/>
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80 <param name="minscore" value="30"/>
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81 <param name="reverse" value="no"/>
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82 <param name="splice" value="yes"/>
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83 <param name="mode" value="both"/>
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84 <param name="best" value="yes"/>
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85 <param name="shuffle" value="0"/>
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86 <param name="seed" value="20825"/>
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87 <param name="align" value="no"/>
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88 <param name="width" value="50"/>
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89 <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
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90 </test>
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91 </tests>
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92 <help>
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93 .. class:: warningmark
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94
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95 The input dataset needs to be sequences.
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96
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97 -----
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98
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99 You can view the original documentation here_.
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100
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101 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html
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102
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103 ------
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104
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105 **Citation**
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106
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107 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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108
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109 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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110 </help>
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111 </tool>