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annotate glimmer_w_icm.xml @ 0:9b2e283dc3b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:10:55 -0500
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1 <tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
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2 <description>Predict ORFs in prokaryotic genomes (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 detect_errors="aggressive"><![CDATA[
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8 glimmer3
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9 --max_olap $max_olap
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10 --gene_len $gene_len
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11 --threshold $threshold
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12 #if float( str($gc_percent) ) > 0.0:
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13 --gc_percent $gc_percent
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14 #end if
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15
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16 #if $stop_codon_opts.stop_codon_opts_selector == "gb":
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17 --trans_table '${stop_codon_opts.genbank_gencode}'
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18 #else:
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19 --stop_codons '${stop_codon_opts.stop_codons}'
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20 #end if
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21
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22 --start_codons '$start_codons'
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23
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24 $linear
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25 $no_indep
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26 $extend
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27 '$seq_input'
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28 '$icm_input'
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29 glimmer_output
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30
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31 &&
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32
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33 #if $report:
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34 cp glimmer_output.predict '$report_output' &&
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35 #end if
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36 #if $detailed_report:
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37 cp glimmer_output.detail '$detailed_output' &&
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38 #end if
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39
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40 ## convert prediction to FASTA sequences
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41 python '$__tool_directory__/glimmer2seq.py' glimmer_output.predict '$seq_input' '$genes_output'
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42 ]]></command>
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43 <inputs>
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44 <param name="seq_input" type="data" format="fasta" label="Genome Sequence" />
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45 <param name="icm_input" type="data" format="tar" label="Interpolated context model (ICM)" />
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46
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47 <param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." />
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48 <param name="gene_len" type="integer" value="90" label="Set the minimum gene length to n nucleotides" help="This does not include the bases in the stop codon."/>
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49 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene" help="If the in-frame score >= N, then the region is given a number and considered a potential gene." />
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50 <param name="gc_percent" type="float" value="0.0" label="Set the GC percentage of the independent model, i.e., the model of intergenic sequence" help="If 0.0 specified, the GC percentage will be counted from the input file." />
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51
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52 <param name="linear" type="boolean" truevalue="--linear" falsevalue="" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
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53 <param name="no_indep" type="boolean" truevalue="--no_indep" falsevalue="" checked="false" label="Don’t use the independent probability score column at all" help="Using this option will produce more short gene predictions." />
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54 <param name="extend" type="boolean" truevalue="--extend" falsevalue="" checked="false" label="Also score orfs that extend off the end of the sequence(s)" />
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55 <param name="start_codons" type="text" value="atg,gtg,ttg" label="Specify start codons as a comma-separated list" />
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56
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57 <conditional name="stop_codon_opts">
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58 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
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59 <option value="gb" selected="True">Genbank translation table entry</option>
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60 <option value="free_form">Comma-separated list</option>
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61 </param>
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62 <when value="gb">
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63 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
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64 <option value="1" selected="True">1. Standard</option>
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65 <option value="2">2. Vertebrate Mitochondrial</option>
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66 <option value="3">3. Yeast Mitochondrial</option>
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67 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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68 <option value="5">5. Invertebrate Mitochondrial</option>
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69 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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70 <option value="9">9. Echinoderm Mitochondrial</option>
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71 <option value="10">10. Euplotid Nuclear</option>
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72 <option value="11">11. Bacteria and Archaea</option>
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73 <option value="12">12. Alternative Yeast Nuclear</option>
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74 <option value="13">13. Ascidian Mitochondrial</option>
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75 <option value="14">14. Flatworm Mitochondrial</option>
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76 <option value="15">15. Blepharisma Macronuclear</option>
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77 <option value="16">16. Chlorophycean Mitochondrial</option>
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78 <option value="21">21. Trematode Mitochondrial</option>
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79 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
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80 <option value="23">23. Thraustochytrium Mitochondrial</option>
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81 <option value="24">24. Pterobranchia mitochondrial</option>
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82 </param>
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83 </when>
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84 <when value="free_form">
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85 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
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86 </when>
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87 </conditional>
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88
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89 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
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90 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
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91 </inputs>
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92 <outputs>
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93 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
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94 <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
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95 <filter>report == True</filter>
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96 </data>
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97 <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
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98 <filter>detailed_report == True</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <test>
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103 <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
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104 <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
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105 <param name="max_olap" value="50" />
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106 <param name="gene_len" value="90" />
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107 <param name="threshold" value="30" />
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108 <param name="gc_percent" value="0.0" />
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109 <param name="linear" value="--linear" />
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110 <param name="no_indep" value="" />
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111 <param name="extend" value="" />
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112 <param name="start_codons" value="atg,gtg,ttg" />
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113 <param name="genbank_gencode" value="11" />
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114 <param name="detailed_report" value="true" />
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115 <param name="report" value="true" />
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116 <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
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117 <output name="report_output" file='glimmer_w_icm_trans-table-11_genomic.out' ftype="txt" />
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118 <output name="detailed_output" file='glimmer_w_icm_trans-table-11_genomic.dout' ftype="txt" lines_diff="6" />
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119 </test>
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120 </tests>
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121 <help><![CDATA[
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122 **What it does**
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123
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124 This is the main program that makes gene predictions based on an interpolated context model (ICM).
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125
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126 The ICM can be generated with extracted CDS from related organisms (ICM builder). If you can't generate an ICM model you can use the non knowlegde-based Glimmer with a de novo prediction.
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127
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128
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129 **Input**
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130
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131 - Interpolated context model (ICM): Use the 'Glimmer ICM builder' tool to create one
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132 - Genome Sequence in FASTA format
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133
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134
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135
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136 **Output**
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137
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138 - FASTA file with predicted proteins
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139 - Glimmer prediction file (optional)
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140 ]]></help>
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141 <expand macro="citation" />
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142 </tool>