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mvdbeek
8337f55e21
and use single-quotes for path, remove deprecated inpterpreter attribute. Fixes https://jenkins.galaxyproject.org/job/docker-main-tools-py3/248/
98 lines
4.6 KiB
XML
98 lines
4.6 KiB
XML
<tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
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<description>converter</description>
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<edam_operations>
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<edam_operation>operation_3434</edam_operation>
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</edam_operations>
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<command>python '$__tool_directory__/bed_to_gff_converter.py' '$input' '$out_file1'</command>
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<inputs>
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<param format="bed" name="input" type="data" label="Convert this dataset"/>
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</inputs>
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<outputs>
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<data format="gff" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="9.bed"/>
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<output name="out_file1">
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<assert_contents>
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<has_line line="chr28	bed2gff	mRNA	346188	388197	0	+	.	mRNA BC114771;"/>
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<has_line line="chr28	bed2gff	exon	388086	388197	0	+	.	exon BC114771;"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help>
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**What it does**
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This tool converts data from BED format to GFF format (scroll down for format description).
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--------
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**Example**
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The following data in BED format::
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chr28 346187 388197 BC114771 0 + 346187 388197 0 9 144,81,115,63,155,96,134,105,112, 0,24095,26190,31006,32131,33534,36994,41793,41898,
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Will be converted to GFF (**note** that the start coordinate is incremented by 1)::
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##gff-version 2
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##bed_to_gff_converter.py
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chr28 bed2gff mRNA 346188 388197 0 + . mRNA BC114771;
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chr28 bed2gff exon 346188 346331 0 + . exon BC114771;
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chr28 bed2gff exon 370283 370363 0 + . exon BC114771;
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chr28 bed2gff exon 372378 372492 0 + . exon BC114771;
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chr28 bed2gff exon 377194 377256 0 + . exon BC114771;
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chr28 bed2gff exon 378319 378473 0 + . exon BC114771;
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chr28 bed2gff exon 379722 379817 0 + . exon BC114771;
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chr28 bed2gff exon 383182 383315 0 + . exon BC114771;
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chr28 bed2gff exon 387981 388085 0 + . exon BC114771;
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chr28 bed2gff exon 388086 388197 0 + . exon BC114771;
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------
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.. class:: informark
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**About formats**
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**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:
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The first three BED fields (required) are::
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1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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The additional BED fields (optional) are::
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4. name - The name of the BED line.
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5. score - A score between 0 and 1000.
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6. strand - Defines the strand - either '+' or '-'.
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7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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9. reserved - This should always be set to zero.
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10. blockCount - The number of blocks (exons) in the BED line.
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11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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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.
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13. expCount - The number of experiments.
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14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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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.
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**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::
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1. seqname - Must be a chromosome or scaffold.
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2. source - The program that generated this feature.
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3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
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4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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5. end - The ending position of the feature (inclusive).
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6. score - A score between 0 and 1000. If there is no score value, enter ".".
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7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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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 '.'.
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9. group - All lines with the same group are linked together into a single item.
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</help>
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</tool>
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