Mercurial > repos > vipints > fml_mergeloci

comparison fml_gff_groomer/galaxy/gff_loci_merge.xml @ 0:79726c328621 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:79726c328621
1 <tool id="fml_mergeloci" name="MergeLoci" version="1.0.0">
2 <description>Merge feature annotation from same loci</description>
3 <command interpreter="python">
4 gff_loci_merge.py
5 $gff_input
6 $gff_result
7 > $logfile
8 </command>
9 <inputs>
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."/>
11 </inputs>
12 <outputs>
13 <data format="txt" name="logfile" label="Log file for MergeLoci" />
14 <data format="gff3" name="gff_result" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="gff_input" value="ucsc_splitted_genes.gff3" />
19 <output name="logfile" file="ucsc_merged_genes_log.txt" />
20 <output name="gff_result" file="ucsc_merged_genes.gff3" />
21 </test>
22 </tests>
23 <help>
24
25 **What it does**
26
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.
28
29 --------
30
31 **Example**
32
33 - data in GFF3 format::
34
35 ##gff-version 3
36 chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1
37 chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1
38 chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
39 chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
40 chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
41 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
42 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
43 chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
44 chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
45 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
46 chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
47 chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
48 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
49 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
50 chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1
51 chr19 hg19_knownGene gene 44770351 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1
52 chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1
53 chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
54 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
55 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
56 chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
57 chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
58 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
59 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
60 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
61 chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
62 chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1
63
64 - Will be merged as::
65
66 ##gff-version 3
67 chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene_hg19_chr19_00001;Name=Gene_hg19_chr19_0001
68 chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene_hg19_chr19_0001
69 chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
70 chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
71 chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
72 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
73 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
74 chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
75 chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
76 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
77 chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1
78 chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1
79 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
80 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
81 chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1
82 chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Gene_hg19_chr19_0001
83 chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1
84 chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
85 chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
86 chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
87 chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1
88 chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1
89 chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1
90 chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1
91 chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1
92 chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1
93
94 --------
95
96 **About formats**
97
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:
99
100 1. seqid - Must be a chromosome or scaffold.
101 2. source - The program that generated this feature.
102 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
103 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
104 5. stop - The ending position of the feature (inclusive).
105 6. score - A score between 0 and 1000. If there is no score value, enter ".".
106 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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 '.'.
108 9. attributes - All lines with the same group are linked together into a single item.
109
110 --------
111
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)
113 </help>
114 </tool>