Mercurial > repos > earlhaminst > gstf_preparation

annotate gstf_preparation.xml @ 13:51a7a2a82902 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9178f870760132962f8d3a26ea55c201880bb018-dirty"
author earlhaminst
date Tue, 06 Oct 2020 17:10:37 +0000
parents 99bae410128c
children
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99bae410128c "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 4579d0c461c30183a3092d84013e30f53f072ca1-dirty"
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1 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.3">
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2 <description>converts data for the workflow</description>
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/gstf_preparation.py'
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8 #for $q in $queries
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9 --gff3 '${q.genome}:${q.gff3_input}'
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10 #end for
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11 #if str($json) != 'None'
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12 #for $v in $json
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13 --json '$v'
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14 #end for
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15 #end if
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16 #for $fasta_input in $fasta_inputs
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17 --fasta '${fasta_input}'
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18 #end for
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19 #if $headers
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20 --headers $headers
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21 #end if
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22 #if $filter
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23 --filter $filter
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24 #end if
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25 #if $regions
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26 --regions '$regions'
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27 --ff '$filtered_fasta'
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28 #end if
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29 -o '$output_db'
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30 --of '$output_fasta'
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31 ]]></command>
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33 <inputs>
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34 <repeat name="queries" title="GFF3 dataset">
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35 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
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36 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
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37 <validator type="empty_field" />
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38 </param>
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39 </repeat>
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40 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
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41 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
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42 <param name="filter" type="select" display="radio" label="Which transcripts to keep">
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43 <option value="canonical" selected="true">Only canonical transcripts (or longest CDS per gene)</option>
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44 <option value="coding">Only protein-coding transcripts</option>
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45 <option value="">All transcripts</option>
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46 </param>
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47
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48 <param name="headers" type="select" display="radio" label="Change the header line of the FASTA sequences to the following format" help="As required by TreeBest, part of the GeneSeqToFamily workflow, only TranscriptId_species is acceptable format by Aequatus visualisation">
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49 <option value="TranscriptId_species" selected="true">TranscriptId_species</option>
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50 <option value="TranscriptID-GeneSymbol_species">TranscriptID-GeneSymbol_species</option>
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51 <option value="TranscriptID-TranscriptSymbol_species">TranscriptID-TranscriptSymbol_species</option>
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52 <option value="">Don't change</option>
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53 </param>
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54 <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered out" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter out chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
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55 </inputs>
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56
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57 <outputs>
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58 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
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59 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
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60 <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences">
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61 <filter>regions</filter>
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62 </data>
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63 </outputs>
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64
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65 <tests>
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66 <test expect_num_outputs="2">
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67 <repeat name="queries">
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68 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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69 <param name="genome" value="caenorhabditis_elegans" />
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70 </repeat>
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71 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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72 <param name="filter" value="coding" />
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73 <param name="headers" value="TranscriptId_species" />
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74
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75 <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
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76 <output name="output_fasta" file="test1.fasta" />
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77 </test>
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78 <test expect_num_outputs="2">
11
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earlhaminst
parents: 10
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79 <repeat name="queries">
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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80 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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81 <param name="genome" value="caenorhabditis_elegans" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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82 </repeat>
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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83 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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84 <param name="filter" value="canonical" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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85 <param name="headers" value="TranscriptId_species" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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86
10
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earlhaminst
parents: 8
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87 <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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88 <output name="output_fasta" file="test1_longest.fasta" />
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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89 </test>
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
earlhaminst
parents: 8
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90 <test expect_num_outputs="2">
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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91 <param name="json" ftype="gff3" value="gene.json" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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92 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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93 <param name="filter" value="" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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94 <param name="headers" value="" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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95
11
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96 <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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97 <output name="output_fasta" file="CDS.fasta" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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98 </test>
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
earlhaminst
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99 <test expect_num_outputs="2">
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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100 <param name="json" ftype="json" value="gene.json" />
0
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101 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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102 <param name="filter" value="coding" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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103 <param name="headers" value="TranscriptId_species" />
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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104
10
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105 <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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106 <output name="output_fasta" file="test4.fasta" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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107 </test>
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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108 <test>
11
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109 <param name="json" ftype="json" value="gene.json" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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110 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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111 <param name="filter" value="coding" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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112 <param name="headers" value="TranscriptId_species" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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113 <param name="regions" value="X" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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114
10
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115 <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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116 <output name="output_fasta" file="test5_filtered.fasta" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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117 <output name="filtered_fasta" file="test5.ns.fasta" />
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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118 </test>
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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119 <test expect_num_outputs="2">
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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120 <repeat name="queries">
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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121 <param name="gff3_input" ftype="gff3" value="MGP_PahariEiJ_G0008413.1.gff3" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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122 <param name="genome" value="mus_pahari" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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123 </repeat>
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
earlhaminst
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124 <param name="fasta_inputs" ftype="fasta" value="Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa" />
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
earlhaminst
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125 <param name="filter" value="canonical" />
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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126 <param name="headers" value="TranscriptId_species" />
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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127
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
earlhaminst
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128 <output name="output_db" file="test6.sqlite" compare="sim_size" delta="30000" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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129 <output name="output_fasta" file="test6.fasta" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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130 </test>
0
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131 </tests>
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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132 <help><![CDATA[
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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133 **What it does**
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134
4
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135 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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136
11
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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137 It also filters the CDS FASTA datasets to keep only the transcripts present in the gene feature information.
8
92f3966d5bc3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 88ba62ae8c3d9587a0015c72209242ad0c1df0c2
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138
11
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139 Optionally it can also:
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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140 - keep only canonical transcripts (or the longest CDS per gene, if this attribute is not provided)
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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141 - remove sequences which are annotated as non protein-coding or whose length is not a multiple of 3
dbe37a658cd2 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 133a11e7195f8da83c5b661d8babb3f6d9e18812"
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142 - change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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143
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144 Example GFF3 file::
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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145
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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146 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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147 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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148 scaffold_0 MYZPE13164_Clone_G006_v1.0 three_prime_utr 44968 46637 . - . ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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149 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 44968 47432 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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150 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 46638 47432 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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151 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 53325 53539 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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152 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 53325 53539 . - 2 ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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153 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54614 54719 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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154 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54614 54719 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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155 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54852 55106 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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156 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54852 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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157 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 55107 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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158 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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159 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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160
2
19644996bc2a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 3f85b0698a37f8fd5404df4044e891949357c011-dirty
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161 The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** attributes in the 9th column are needed to create relations among features.
19644996bc2a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 3f85b0698a37f8fd5404df4044e891949357c011-dirty
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162
19644996bc2a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 3f85b0698a37f8fd5404df4044e891949357c011-dirty
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163 .. class:: warningmark
19644996bc2a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 3f85b0698a37f8fd5404df4044e891949357c011-dirty
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164
19644996bc2a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 3f85b0698a37f8fd5404df4044e891949357c011-dirty
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165 If a value in the **ID** and **Parent** attribute contains a colon, everything up to the first colon will be discarded.
10
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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166 ]]></help>
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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167 <citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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168 </citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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169 </tool>