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annotate glimmer_wo_icm.xml @ 0:4da5f6bdcf12 draft

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author bgruening
date Tue, 28 Nov 2017 10:10:13 -0500
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1 <tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
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2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8 python '$__tool_directory__/glimmer_wo_icm.py'
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9 '$input'
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10 #if $report:
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11 '$prediction'
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12 #else:
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13 'None'
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14 #end if
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15 #if $detailed_report:
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16 '$detailed'
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17 #else:
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18 'None'
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19 #end if
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20 $overlap
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21 $gene_length
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22 $threshold
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23 $linear
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24 '$genes_output'
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25 ]]></command>
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26 <inputs>
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27 <param name="input" type="data" format="fasta" label="Genome sequence" />
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28 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." />
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29 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." />
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30 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." />
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31 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
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32
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33 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" />
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34 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" />
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35 </inputs>
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36 <outputs>
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37 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
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38 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
4da5f6bdcf12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 <filter>report == True</filter>
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40 </data>
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41 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
4da5f6bdcf12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42 <filter>detailed_report == True</filter>
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43 </data>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
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48 <param name="overlap" value="0" />
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49 <param name="gene_length" value="110" />
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50 <param name="threshold" value="30" />
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51 <param name="linear" value="true" />
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52 <param name="detailed_report" value="" />
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53 <param name="report" value="" />
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54 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
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55 </test>
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56 </tests>
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57 <help>
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58 <![CDATA[
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59
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60 **What it does**
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61
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62 This tool predicts open reading frames (ORFs) from a given DNA Sequence. That tool is not knowlegde-based.
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63
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64 The recommended way is to use a trained Glimmer3 with ICM model. Use the knowlegde-based version for that and insert/generate a training set.
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65
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66 -----
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67
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68 **Glimmer Overview**
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69
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70 ::
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71
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72 ************** ************** ************** **************
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73 * * * * * * * *
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74 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
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75 * * * * * * * *
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76 ************** ************** ************** **************
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77
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78 -----
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80 **Example**
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81
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82 Suppose you have the following DNA sequences::
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83
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84 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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85 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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86 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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87 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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88 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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89 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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90 .......
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91
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92 Running this tool will produce a FASTA file with predicted genes and glimmer output files like the following::
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93
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94 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
4da5f6bdcf12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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95 orf00001 577 699 +1 5.24
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96 orf00003 800 1123 +2 5.18
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97 orf00004 1144 3813 +1 10.62
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98 orf00006 3857 6220 +2 6.07
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99 orf00007 6226 7173 +1 1.69
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100 orf00008 7187 9307 +2 8.95
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101 orf00009 9424 10410 +1 8.29
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102 orf00010 10515 11363 +3 7.00
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103 orf00011 11812 11964 +1 2.80
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104 orf00012 12360 13457 +3 4.80
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105 orf00013 14379 14044 -1 7.41
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106 orf00015 15029 14739 -3 12.43
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107 orf00016 15066 15227 +3 1.91
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108 orf00020 16061 15351 -3 2.83
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109 orf00021 17513 17391 -3 2.20
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110 orf00023 17529 17675 +3 0.11
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111
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112
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113
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114 ]]>
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115 </help>
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116 <expand macro="citation" />
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117 </tool>