annotate windowSplitter.xml @ 2:592089499ae7 draft

planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d

<tool id="winSplitter" name="Make windows" version="1.0.0">
  <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" 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" 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>