Mercurial > repos > petr-novak > various_galaxy_tools

annotate gff2bed.xml @ 3:1069776f7ae2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 3b9f93ed06cc32dbfa271789739e7a1e8fac528c
author petr-novak
date Tue, 30 Apr 2024 08:27:27 +0000
parents 90c46e40d222
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
diff changeset
1 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.2">
0
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
2 <description>converter</description>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
3 <edam_operations>
2
90c46e40d222 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 1
diff changeset
4 <edam_operation>operation_3434</edam_operation>
0
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
5 </edam_operations>
2
90c46e40d222 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 1
diff changeset
6 <required_files>
90c46e40d222 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 1
diff changeset
7 <include type="literal" path="gff_to_bed_converter.py"/>
90c46e40d222 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 1
diff changeset
8 </required_files>
1
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
diff changeset
9 <command>
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
diff changeset
10 python '$__tool_directory__'/gff_to_bed_converter.py $input $out_file1
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
diff changeset
11 </command>
0
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
12 <inputs>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
13 <param format="gff" name="input" type="data" label="Convert this dataset"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
14 </inputs>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
15 <outputs>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
16 <data format="bed" name="out_file1" />
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
17 </outputs>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
18 <tests>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
19 <test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
20 <param name="input" value="5.gff" ftype="gff"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
21 <output name="out_file1" file="gff2bed_out.bed"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
22 </test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
23 <test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
24 <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
25 <output name="out_file1" file="gff2bed_out2.bed"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
26 </test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
27 <test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
28 <!-- Test conversion of gff3 file. -->
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
29 <param name="input" value="5.gff3" ftype="gff"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
30 <output name="out_file1" file="gff2bed_out3.bed"/>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
31 </test>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
32 </tests>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
33 <help>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
34
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
35 **What it does**
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
36
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
37 This tool converts data from GFF format to BED format (scroll down for format description).
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
38
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
39 --------
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
40
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
41 **Example**
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
42
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
43 The following data in GFF format::
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
44
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
45 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
46 chr22 GeneA promoter 10010000 10010100 900 + . TGA
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
47
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
48 Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
49
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
50 chr22 9999999 10001000 enhancer 0 +
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
51 chr22 10009999 10010100 promoter 0 +
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
52
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
53 ------
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
54
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
55 .. class:: infomark
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
56
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
57 **About formats**
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
58
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
59 **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:
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
60
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
61 The first three BED fields (required) are::
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
62
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
63 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
64 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
65 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
66
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
67 The additional BED fields (optional) are::
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
68
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
69 4. name - The name of the BED line.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
70 5. score - A score between 0 and 1000.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
71 6. strand - Defines the strand - either '+' or '-'.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
72 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
73 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
74 9. reserved - This should always be set to zero.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
75 10. blockCount - The number of blocks (exons) in the BED line.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
76 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
77 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.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
78 13. expCount - The number of experiments.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
79 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
80 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.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
81
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
82 **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::
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
83
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
84 1. seqname - Must be a chromosome or scaffold.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
85 2. source - The program that generated this feature.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
86 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
87 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
88 5. end - The ending position of the feature (inclusive).
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
89 6. score - A score between 0 and 1000. If there is no score value, enter ".".
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
90 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
91 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 '.'.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
92 9. group - All lines with the same group are linked together into a single item.
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
93
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
94 </help>
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
diff changeset
95 </tool>