/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
- <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>