Mercurial > repos > xuebing > sharplabtool
view tools/regVariation/windowSplitter.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="winSplitter" name="Make windows"> <description></description> <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> <inputs> <!--<param label="Genome" name="dbkey" type="genomebuild"/>--> <param format="interval" name="input" type="data" label="Select data"/> <param name="size" size="10" type="integer" value="500" label="Window size"/> <conditional name="wintype"> <param name="choice" type="select" label="Make sliding windows?"> <option value="0" selected="true">No</option> <option value="1">Yes</option> </param> <when value="0"> <param name="offset" type="hidden" value="0" /> </when> <when value="1"> <param name="offset" size="10" type="integer" value="10" label="Offset size"/> </when> </conditional> </inputs> <outputs> <data format="interval" name="out_file1" metadata_source="input"/> </outputs> <tests> <test> <param name="input" value="4.bed"/> <param name="size" value="5000"/> <param name="choice" value="1"/> <param name="offset" value="4000"/> <output name="out_file1" file="4_windows.bed"/> </test> </tests> <help> .. class:: infomark **What it does** This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type. ----- .. class:: warningmark **Note** 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. ----- .. class:: infomark **About formats** **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: The first three BED fields (required) are:: 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). The additional BED fields (optional) are:: 4. name - The name of the BED line. 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. 9. reserved - This should always be set to zero. 10. blockCount - The number of blocks (exons) in the BED line. 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. 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. 13. expCount - The number of experiments. 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. 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. ----- **Example** - For the following dataset:: chr22 1000 4700 NM_174568 0 + - running this tool with **Window size as 1000**, will return:: chr22 1000 2000 NM_174568 0 + chr22 2000 3000 NM_174568 0 + chr22 3000 4000 NM_174568 0 + - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return:: chr22 1000 2000 NM_174568 0 + chr22 1500 2500 NM_174568 0 + chr22 2000 3000 NM_174568 0 + chr22 2500 3500 NM_174568 0 + chr22 3000 4000 NM_174568 0 + chr22 3500 4500 NM_174568 0 + </help> </tool>