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comparison gff2bed.xml @ 0:696e702ebf74 draft

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"planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
author petr-novak
date Mon, 09 May 2022 08:26:30 +0000
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1 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
2 <description>converter</description>
3 <edam_operations>
4 <edam_operation>operation_3434</edam_operation>
5 </edam_operations>
6 <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
7 <inputs>
8 <param format="gff" name="input" type="data" label="Convert this dataset"/>
9 </inputs>
10 <outputs>
11 <data format="bed" name="out_file1" />
12 </outputs>
13 <tests>
14 <test>
15 <param name="input" value="5.gff" ftype="gff"/>
16 <output name="out_file1" file="gff2bed_out.bed"/>
17 </test>
18 <test>
19 <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
20 <output name="out_file1" file="gff2bed_out2.bed"/>
21 </test>
22 <test>
23 <!-- Test conversion of gff3 file. -->
24 <param name="input" value="5.gff3" ftype="gff"/>
25 <output name="out_file1" file="gff2bed_out3.bed"/>
26 </test>
27 </tests>
28 <help>
29
30 **What it does**
31
32 This tool converts data from GFF format to BED format (scroll down for format description).
33
34 --------
35
36 **Example**
37
38 The following data in GFF format::
39
40 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
41 chr22 GeneA promoter 10010000 10010100 900 + . TGA
42
43 Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
44
45 chr22 9999999 10001000 enhancer 0 +
46 chr22 10009999 10010100 promoter 0 +
47
48 ------
49
50 .. class:: infomark
51
52 **About formats**
53
54 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
55
56 The first three BED fields (required) are::
57
58 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
59 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
60 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
61
62 The additional BED fields (optional) are::
63
64 4. name - The name of the BED line.
65 5. score - A score between 0 and 1000.
66 6. strand - Defines the strand - either '+' or '-'.
67 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
68 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
69 9. reserved - This should always be set to zero.
70 10. blockCount - The number of blocks (exons) in the BED line.
71 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
72 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
73 13. expCount - The number of experiments.
74 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
75 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
76
77 **GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
78
79 1. seqname - Must be a chromosome or scaffold.
80 2. source - The program that generated this feature.
81 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
82 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
83 5. end - The ending position of the feature (inclusive).
84 6. score - A score between 0 and 1000. If there is no score value, enter ".".
85 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
86 8. frame - 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 '.'.
87 9. group - All lines with the same group are linked together into a single item.
88
89 </help>
90 </tool>