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/tools/regVariation/windowSplitter.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 104 lines | 77 code | 26 blank | 1 comment | 0 complexity | 7585c4eb95e074cfdebfbd8491d1fa0b MD5 | raw file
  1<tool id="winSplitter" name="Make windows">
  2  <description></description>
  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>
  4  <inputs>
  5    <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
  6    <param format="interval" name="input" type="data" label="Select data"/>
  7    <param name="size" size="10" type="integer" value="500" label="Window size"/>
  8    <conditional name="wintype">
  9	    <param name="choice" type="select" label="Make sliding windows?">
 10	    	<option value="0" selected="true">No</option>
 11	    	<option value="1">Yes</option>
 12		</param>
 13		<when value="0">
 14    		<param name="offset" type="hidden" value="0" />
 15    	</when>
 16    	<when value="1">
 17    		<param name="offset" size="10" type="integer" value="10" label="Offset size"/>
 18    	</when>
 19	</conditional>
 20  </inputs>
 21  <outputs>
 22    <data format="interval" name="out_file1" metadata_source="input"/>
 23  </outputs>
 24  <tests>
 25    <test>
 26      <param name="input" value="4.bed"/>
 27      <param name="size" value="5000"/>
 28      <param name="choice" value="1"/>
 29      <param name="offset" value="4000"/>
 30      <output name="out_file1" file="4_windows.bed"/>
 31    </test>
 32  </tests>
 33 <help> 
 34
 35.. class:: infomark
 36
 37**What it does**
 38
 39This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
 40
 41-----
 42
 43.. class:: warningmark
 44
 45**Note**
 46
 47The 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.
 48
 49-----
 50
 51.. class:: infomark
 52
 53**About formats**
 54
 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:
 56
 57The first three BED fields (required) are::
 58
 59    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
 60    2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
 61    3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
 62
 63The additional BED fields (optional) are::
 64
 65    4. name - The name of the BED line.
 66    5. score - A score between 0 and 1000.
 67    6. strand - Defines the strand - either '+' or '-'.
 68    7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
 69    8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
 70    9. reserved - This should always be set to zero.
 71   10. blockCount - The number of blocks (exons) in the BED line.
 72   11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
 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.
 74   13. expCount - The number of experiments.
 75   14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
 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.
 77
 78-----
 79
 80**Example**
 81
 82- For the following dataset::
 83
 84   chr22  1000  4700  NM_174568 0 +
 85
 86- running this tool with **Window size as 1000**,  will return::
 87
 88   chr22  1000  2000  NM_174568 0 +
 89   chr22  2000	3000  NM_174568	0 +
 90   chr22  3000  4000  NM_174568 0 +
 91   
 92- running this tool to make **Sliding windows** of **size 1000** and **offset 500**,  will return::
 93
 94   chr22  1000  2000  NM_174568 0 +
 95   chr22  1500	2500  NM_174568	0 +
 96   chr22  2000  3000  NM_174568 0 +
 97   chr22  2500	3500  NM_174568	0 +
 98   chr22  3000  4000  NM_174568 0 +
 99   chr22  3500	4500  NM_174568	0 +
100  
101  </help>  
102
103
104</tool>