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

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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_available_limits" name="FeatureScan" version="1.0.0">
2 <description>gives an overview about GFF file content</description>
3 <command interpreter="python">
4 gff_available_limits.py
5 $gff_input
6 > $overview
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="overview" label="Feature contents in GFF file" />
13 </outputs>
14 <tests>
15 <test>
16 <param name="gff_input" value="GFF_2_Source.gff3" />
17 <output name="overview" file="GFF_2_Source_FeatureScan.txt" />
18 </test>
19 </tests>
20 <help>
21
22 **What it does**
23
24 This tool provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given GFF file.
25
26 --------
27
28 **Example**
29
30 - The features ID mapping in the following data in GFF format::
31
32 ##gff-version 3
33 scaffold_1 JGI_Filtered gene 33131338 33131726 . - . ID=scaffold_105720.1;Name=scaffold_105720.1
34 scaffold_1 JGI_Filtered mRNA 33131338 33131726 . - . ID=Transcript:924439;Name=Transcript:924439;Parent=scaffold_105720.1
35 scaffold_1 JGI_Filtered three_prime_UTR 33131338 33131357 . - . ID=three_prime_UTR:924439;Parent=Transcript:924439
36 scaffold_1 JGI_Filtered exon 33131338 33131654 . - . ID=exon:924439;Parent=Transcript:924439
37 scaffold_1 JGI_Filtered CDS 33131358 33131654 . - 0 ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
38 scaffold_1 JGI_Filtered exon 33131703 33131726 . - . ID=exon:924439;Parent=Transcript:924439
39 scaffold_1 JGI_Filtered CDS 33131703 33131705 . - 0 ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
40 scaffold_1 JGI_Filtered five_prime_UTR 33131706 33131726 . - . ID=five_prime_UTR:924439;Parent=Transcript:924439
41 Chr4 TAIR9 gene 1180 1536 . - . ID=AT4G00005;Note=protein_coding_gene;Name=AT4G00005
42 Chr4 TAIR9 mRNA 1180 1536 . - . ID=AT4G00005.1;Parent=AT4G00005;Name=AT4G00005.1;Index=1
43 Chr4 TAIR9 protein 1180 1536 . - . ID=AT4G00005.1-Protein;Name=AT4G00005.1;Derives_from=AT4G00005.1
44 Chr4 TAIR9 CDS 1180 1536 . - 0 Parent=AT4G00005.1,AT4G00005.1-Protein;
45 Chr4 TAIR9 exon 1180 1536 . - . Parent=AT4G00005.1
46
47 - Will be displayed as::
48
49 Chromosome identifier(s) and corresponding count:
50 Chr4 5
51 scaffold_1 8
52
53 Source(s) of feature and corresponding count:
54 JGI_Filtered 8
55 TAIR9 5
56
57 Feature type(s) and corresponding count:
58 gene 2
59 mRNA 2
60 five_prime_UTR 1
61 three_prime_UTR 1
62 exon 3
63 CDS 3
64 protein 1
65
66 Unique combination of Feature type(s), Source(s) and corresponding count:
67 JGI_Filtered, CDS 2
68 JGI_Filtered, exon 2
69 JGI_Filtered, five_prime_UTR 1
70 JGI_Filtered, gene 1
71 JGI_Filtered, mRNA 1
72 JGI_Filtered, three_prime_UTR 1
73 TAIR9, CDS 1
74 TAIR9, exon 1
75 TAIR9, protein 1
76 TAIR9, mRNA 1
77 TAIR9, gene 1
78
79 --------
80
81 **About formats**
82
83 **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:
84
85 1. seqid - Must be a chromosome or scaffold.
86 2. source - The program that generated this feature.
87 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
88 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
89 5. stop - The ending position of the feature (inclusive).
90 6. score - A score between 0 and 1000. If there is no score value, enter ".".
91 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
92 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 '.'.
93 9. attributes - All lines with the same group are linked together into a single item.
94
95 --------
96
97 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)
98 </help>
99 </tool>