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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler commit 982fe890ba21272719fe6f5cb04707c4c91fca0d
author iuc
date Sun, 15 Sep 2024 10:12:13 +0000
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92d95470befc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler commit 982fe890ba21272719fe6f5cb04707c4c91fca0d
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1 <tool id="evidencemodeler" name="EVidenceModeler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>combines ab intio gene predictions, protein and transcript alignments into gene structures</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 <xrefs>
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7 <xref type="bio.tools">EvidenceModeler</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12
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13 ln -s '$input_genome' ./input_genome.fasta &&
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14 ln -s '$input_predictions' ./input_predictions.gff &&
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15 ln -s '$input_weights' ./input_weights.txt &&
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16 ln -s '$input_proteins' ./input_proteins.gff &&
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17 ln -s '$input_transcript' ./input_transcript.gff &&
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18
92d95470befc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler commit 982fe890ba21272719fe6f5cb04707c4c91fca0d
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19 EVidenceModeler
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20 --sample_id galaxy
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21 --genome './input_genome.fasta'
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22 --gene_predictions './input_predictions.gff'
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23 --weights './input_weights.txt'
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24 --protein_alignments './input_proteins.gff'
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25 --segmentSize $segmentsize
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26 --overlapSize $overlapsize
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27
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28 #if $input_transcript:
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29 --transcript_alignments './input_transcript.gff'
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30 #end if
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31
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32 #if $opt.input_repeat:
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33 --repeats '$opt.input_repeat'
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34 #end if
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35
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36 #if $opt.input_terminalexon:
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37 --terminalExons '$opt.input_terminalexon'
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38 #end if
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39
92d95470befc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler commit 982fe890ba21272719fe6f5cb04707c4c91fca0d
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40 --stop_codons $opt.stop_codon
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41 --min_intron_length $opt.min_intron_length
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42 --search_long_introns $opt.search_long_introns
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43 --re_search_intergenic $opt.re_search_intergenic
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44 --terminal_intergenic_re_search $opt.terminal_intergenic_re_search
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45
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46 ]]></command>
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47
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48 <inputs>
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49 <param name="input_genome" type="data" format="fasta" label="Genome input"/>
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50 <param name="input_predictions" type="data" format="gff3" label="Gene predictions input"/>
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51 <param name="input_weights" type="data" format="gff3" label="Weights for evidence types file" help="See documentation for formatting: 'Weights' section"/>
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52 <param name="input_proteins" type="data" format="gff3" label="Protein alignments input" help="Optional but recommended"/>
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53 <param name="input_transcript" type="data" optional="true" format="gff3" label="Transcript alignments input" help="Optional but recommended"/>
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54 <param argument="--segmentSize" name="segmentsize" value="100000" type="integer" label="Length of a single sequence" help="This value must be less than 1 MB" />
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55 <param argument="--overlapSize" name="overlapsize" value="10000" type="integer" label="Length of sequence overlap between segmented sequences" help="The length must be at least equivalent to one or two expected gene lengths" />
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56 <section name="opt" title="Advanced option" expanded="false">
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57 <param name="input_repeat" type="data" optional="true" format="gff3" label="Masked genome repeats"/>
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58 <param name="input_terminalexon" type="data" optional="true" format="gff3" label="Additional file of terminal exons to be taken into account" help="From long-orfs PASA"/>
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59 <param name="stop_codon" argument="--stop_codons" type="select" multiple="true" optional="true" label="List of stop codon" help="For Tetrahymena, set TGA">
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60 <option value="TAA,TGA,TAG" selected="true">TAA,TGA,TAG</option>
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61 <option value="TAA">TAA</option>
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62 <option value="TGA">TGA</option>
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63 <option value="TAG">TAG</option>
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64 </param>
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65 <param argument="--min_intron_length" type="integer" value="20" label="Minimum length for an intron" help="Default 20 bp" />
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66 <param argument="--search_long_introns" type="select" label="Reexamine long introns" help="Can find nested genes, but also can result in false positives">
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67 <option value="0" selected="true">Off</option>
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68 <option value="1">On</option>
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69 </param>
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70 <param argument="--re_search_intergenic" type="select" label="Reexamines intergenic regions of minimum length">
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71 <option value="0" selected="true">Off</option>
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72 <option value="1">On</option>
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73 </param>
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74 <param argument="--terminal_intergenic_re_search" type="select" label="Reexamines intergenic regions of minimum length">
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75 <option value="0" selected="true">Off</option>
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76 <option value="1">On</option>
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77 </param>
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78 </section>
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79 </inputs>
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80
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81 <outputs>
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82 <data name='evm_gff' format='gff' label="${tool.name} on ${on_string}: GFF3" from_work_dir="galaxy.EVM.gff3"/>
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83 <data name='evm_pep' format='fasta' label="${tool.name} on ${on_string}: PEP" from_work_dir="galaxy.EVM.pep"/>
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84 </outputs>
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85
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86 <tests>
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87 <test expect_num_outputs="2">
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88 <param name="input_genome" value="genome.fasta"/>
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89 <param name="input_predictions" value="gene_predictions.gff3"/>
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90 <param name="input_weights" value="weights.txt"/>
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91 <param name="input_proteins" value="protein_alignments.gff3"/>
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92 <param name="input_transcript" value="transcript_alignments.gff3"/>
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93 <param name="segmentsize" value="100000"/>
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94 <param name="overlapsize" value="10000"/>
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95 <conditional name="opt">
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96 <param name="adv" value="true"/>
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97 <param name="min_intron_length" value="20"/>
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98 <param name="search_long_introns" value="0"/>
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99 <param name="re_search_intergenic" value="0"/>
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100 <param name="terminal_intergenic_re_search" value="0"/>
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101 </conditional>
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102 <output name="evm_pep" ftype="fasta">
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103 <assert_contents>
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104 <has_text text="evm.model.Contig1.3 evm.TU.Contig1.3 EVM prediction Contig1.3 Contig1:7611-9749(-)"/>
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105 <has_text text="evm.model.Contig1.10 evm.TU.Contig1.10 EVM prediction Contig1.10 Contig1:57371-59941(+)"/>
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106 <has_n_lines n="108" delta="0"/>
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107 <has_n_columns n="1" delta="0"/>
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108 </assert_contents>
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109 </output>
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110 <output name="evm_gff" ftype="gff">
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111 <assert_contents>
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112 <has_text text="ID=evm.TU.Contig1.1;Name=EVM%20prediction%20Contig1.1"/>
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113 <has_text text="ID=evm.TU.Contig1.4;Name=EVM%20prediction%20Contig1.4"/>
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114 <has_n_lines n="191" delta="0"/>
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115 <has_n_columns n="9" delta="0"/>
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116 <!-- the sep=";" is used to count the gff properties -->
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117 <has_n_columns n="2" delta="0" sep=";"/>
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118 </assert_contents>
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119 </output>
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120 </test>
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121 </tests>
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122
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123 <help><![CDATA[
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124 EvidenceModeler_: EVidenceModeler (aka EVM) is a software package that combines ab intio
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125 gene predictions and protein and transcript alignments into weighted consensus gene structures.
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126 EVM provides a flexible and intuitive framework for combining various types of evidence into a
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127 single automated gene structure annotation system.
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128
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129 .. _EvidenceModeler: https://github.com/EVidenceModeler/EVidenceModeler.github.io
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130 ]]></help>
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131 <expand macro="citation"></expand>
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132 </tool>