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1 <tool id="gene2intron1" name="Gene BED To Intron BED">
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2 <description>expander</description>
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3 <command interpreter="python">ucsc_gene_bed_to_intron_bed.py --input=$input1 --output=$out_file1</command>
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4 <inputs>
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5 <param name="input1" type="data" format="interval" label="UCSC Gene Table"/>
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6
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7 </inputs>
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8 <outputs>
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9 <data name="out_file1" format="bed"/>
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input1" value="3.bed" />
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14 <output name="out_file1" file="cf-gene2intron.dat"/>
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15 </test>
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16 </tests>
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17 <help>
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18
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19 **Syntax**
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20
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21 This tool converts a UCSC gene bed format file to a list of bed format lines corresponding to requested features of each gene.
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22
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23 - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and twelve additional optional ones::
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24
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25 The first three BED fields (required) are:
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26 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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27 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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28 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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29
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30 The twelve additional BED fields (optional) are:
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31 4. name - The name of the BED line.
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32 5. score - A score between 0 and 1000.
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33 6. strand - Defines the strand - either '+' or '-'.
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34 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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35 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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36 9. reserved - This should always be set to zero.
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37 10. blockCount - The number of blocks (exons) in the BED line.
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38 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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39 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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40 13. expCount - The number of experiments.
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41 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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42 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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43
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44 -----
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45
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46 **Example**
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47
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48 - A UCSC gene bed format file::
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49
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50 chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126
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51 chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399
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52
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53 - Converts the above file to a list of bed lines, which has the introns::
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54
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55 chr7 127475311 127475993 NM_000230 0 +
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56 chr7 127486167 127488406 NM_000230 0 +
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57 chr7 127486167 127488409 D49487 0 +
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58
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59 </help>
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60 </tool>
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