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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