[2] | 1 | <tool id="winSplitter" name="Make windows"> |
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| 2 | <description></description> |
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| 3 | <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command> |
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| 4 | <inputs> |
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| 5 | <!--<param label="Genome" name="dbkey" type="genomebuild"/>--> |
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| 6 | <param format="interval" name="input" type="data" label="Select data"/> |
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| 7 | <param name="size" size="10" type="integer" value="500" label="Window size"/> |
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| 8 | <conditional name="wintype"> |
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| 9 | <param name="choice" type="select" label="Make sliding windows?"> |
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| 10 | <option value="0" selected="true">No</option> |
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| 11 | <option value="1">Yes</option> |
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| 12 | </param> |
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| 13 | <when value="0"> |
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| 14 | <param name="offset" type="hidden" value="0" /> |
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| 15 | </when> |
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| 16 | <when value="1"> |
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| 17 | <param name="offset" size="10" type="integer" value="10" label="Offset size"/> |
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| 18 | </when> |
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| 19 | </conditional> |
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| 20 | </inputs> |
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| 21 | <outputs> |
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| 22 | <data format="interval" name="out_file1" metadata_source="input"/> |
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| 23 | </outputs> |
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| 24 | <tests> |
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| 25 | <test> |
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| 26 | <param name="input" value="4.bed"/> |
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| 27 | <param name="size" value="5000"/> |
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| 28 | <param name="choice" value="1"/> |
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| 29 | <param name="offset" value="4000"/> |
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| 30 | <output name="out_file1" file="4_windows.bed"/> |
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| 31 | </test> |
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| 32 | </tests> |
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| 33 | <help> |
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| 34 | |
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| 35 | .. class:: infomark |
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| 36 | |
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| 37 | **What it does** |
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| 38 | |
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| 39 | This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type. |
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| 40 | |
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| 41 | ----- |
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| 42 | |
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| 43 | .. class:: warningmark |
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| 44 | |
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| 45 | **Note** |
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| 46 | |
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| 47 | The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output. |
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| 48 | |
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| 49 | ----- |
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| 50 | |
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| 51 | .. class:: infomark |
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| 52 | |
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| 53 | **About formats** |
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| 54 | |
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| 55 | **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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| 56 | |
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| 57 | The first three BED fields (required) are:: |
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| 58 | |
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| 59 | 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). |
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| 60 | 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) |
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| 61 | 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). |
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| 62 | |
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| 63 | The additional BED fields (optional) are:: |
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| 64 | |
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| 65 | 4. name - The name of the BED line. |
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| 66 | 5. score - A score between 0 and 1000. |
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| 67 | 6. strand - Defines the strand - either '+' or '-'. |
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| 68 | 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. |
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| 69 | 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. |
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| 70 | 9. reserved - This should always be set to zero. |
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| 71 | 10. blockCount - The number of blocks (exons) in the BED line. |
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| 72 | 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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| 73 | 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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| 74 | 13. expCount - The number of experiments. |
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| 75 | 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. |
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| 76 | 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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| 77 | |
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| 78 | ----- |
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| 79 | |
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| 80 | **Example** |
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| 81 | |
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| 82 | - For the following query:: |
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| 83 | |
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| 84 | chr22 1000 4700 NM_174568 0 + |
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| 85 | |
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| 86 | - running this tool with **Window size as 1000**, will return:: |
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| 87 | |
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| 88 | chr22 1000 2000 NM_174568 0 + |
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| 89 | chr22 2000 3000 NM_174568 0 + |
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| 90 | chr22 3000 4000 NM_174568 0 + |
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| 91 | |
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| 92 | - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return:: |
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| 93 | |
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| 94 | chr22 1000 2000 NM_174568 0 + |
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| 95 | chr22 1500 2500 NM_174568 0 + |
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| 96 | chr22 2000 3000 NM_174568 0 + |
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| 97 | chr22 2500 3500 NM_174568 0 + |
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| 98 | chr22 3000 4000 NM_174568 0 + |
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| 99 | chr22 3500 4500 NM_174568 0 + |
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| 100 | |
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| 101 | </help> |
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| 102 | |
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| 103 | |
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| 104 | </tool> |
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