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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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1 <tool id="gff_parent_child_relation" name="Examine" version="1.0.0">
2 <description>Parent-Child relation in GFF file</description>
3 <command interpreter="python">
4 gff_id_mapper.py
5 $gff_input
6 > $idmapping
7 </command>
8 <inputs>
9 <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 and other features for the provided genome."/>
10 </inputs>
11 <outputs>
12 <data format="txt" name="idmapping" label="Parent-child relation in GFF file" />
13 </outputs>
14 <tests>
15 <test>
16 <param name="gff_input" value="Feature_ID_mapping_W.gff3" />
17 <output name="idmapping" file="Feature_ID_mapping_W.txt" />
18 </test>
19 <test>
20 <param name="gff_input" value="Aly_JGI.gff3" />
21 <output name="idmapping" file="Feature_ID_mapping_R.txt" />
22 </test>
23 </tests>
24 <help>
25
26 **What it does**
27
28 This tool provides the features(gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a given GFF file.
29
30 --------
31
32 **Example**
33
34 - The features ID mapping in the following data in GFF format::
35
36 ##gff-version 3
37 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
38 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
39 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
40 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
41 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
42 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
43
44 - Will be displayed as::
45
46 FIRST level feature(s):
47 ('protein_coding', 'gene')
48
49 SECOND level feature(s):
50 ('protein_coding', 'mRNA')
51
52 THIRD level feature(s):
53 ('protein_coding', 'CDS'), ('protein_coding', 'exon'), ('protein_coding', 'five_prime_UTR'), ('protein_coding', 'three_prime_UTR')
54
55 --------
56
57 **About formats**
58
59 **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:
60
61 1. seqid - Must be a chromosome or scaffold.
62 2. source - The program that generated this feature.
63 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
64 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
65 5. stop - The ending position of the feature (inclusive).
66 6. score - A score between 0 and 1000. If there is no score value, enter ".".
67 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
68 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 '.'.
69 9. attributes - All lines with the same group are linked together into a single item.
70
71 --------
72
73 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)
74 </help>
75 </tool>