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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 17:29:24 -0400
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="fml_mergeloci" name="MergeLoci" version="1.0.0">
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2 <description>Merge feature annotation from same loci</description>
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3 <command interpreter="python">
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4 gff_loci_merge.py
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5 $gff_input
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6 $gff_result
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7 > $logfile
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8 </command>
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9 <inputs>
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10 <param format="gff3" name="gff_input" type="data" label="Genome annotation in GFF3 format" help="Genome annotation in GFF3 format describing the known gene structures for the provided genome."/>
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11 </inputs>
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12 <outputs>
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13 <data format="txt" name="logfile" label="Log file for MergeLoci" />
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14 <data format="gff3" name="gff_result" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="gff_input" value="ucsc_splitted_genes.gff3" />
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19 <output name="logfile" file="ucsc_merged_genes_log.txt" />
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20 <output name="gff_result" file="ucsc_merged_genes.gff3" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25 **What it does**
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26
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27 This tool merge the feature annotation of same loci. MergeLoci will be able to merge several transcripts from single loci to a main feature instead of several features. For example, in UCSC genome annotation files the alternative splice model of the transcript are represented as individual gene models.
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28
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29 --------
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30
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31 **Example**
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32
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33 - data in GFF3 format::
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34
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35 ##gff-version 3
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36 chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1
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37 chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1
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38 chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
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39 chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
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40 chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
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41 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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42 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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43 chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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44 chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
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45 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
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46 chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
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47 chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
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48 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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49 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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50 chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1
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51 chr19 hg19_knownGene gene 44770351 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1
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52 chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1
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53 chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
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54 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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55 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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56 chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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57 chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
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58 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
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59 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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60 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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61 chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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62 chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1
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63
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64 - Will be merged as::
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65
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66 ##gff-version 3
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67 chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene_hg19_chr19_00001;Name=Gene_hg19_chr19_0001
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68 chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene_hg19_chr19_0001
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69 chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
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70 chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
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71 chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
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72 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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73 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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74 chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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75 chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
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76 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
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77 chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
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78 chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
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79 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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80 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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81 chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1
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82 chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Gene_hg19_chr19_0001
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83 chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
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84 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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85 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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86 chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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87 chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
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88 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
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89 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
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90 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
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91 chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
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92 chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1
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93
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94 --------
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95
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96 **About formats**
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97
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98 **GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields:
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99
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100 1. seqid - Must be a chromosome or scaffold.
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101 2. source - The program that generated this feature.
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102 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
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103 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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104 5. stop - The ending position of the feature (inclusive).
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105 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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106 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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107 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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108 9. attributes - All lines with the same group are linked together into a single item.
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109
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110 --------
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111
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112 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)
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113 </help>
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114 </tool>