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104 lines
3.9 KiB
XML
104 lines
3.9 KiB
XML
<tool id="winSplitter" name="Make windows">
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<description></description>
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<command interpreter="python2.4">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command>
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<inputs>
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<!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
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<param format="interval" name="input" type="data" label="Select data"/>
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<param name="size" size="10" type="integer" value="500" label="Window size"/>
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<conditional name="wintype">
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<param name="choice" type="select" label="Make sliding windows?">
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<option value="0" selected="true">No</option>
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<option value="1">Yes</option>
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</param>
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<when value="0">
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<param name="offset" type="hidden" value="0" />
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</when>
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<when value="1">
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<param name="offset" size="10" type="integer" value="10" label="Offset size"/>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" metadata_source="input"/>
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</outputs>
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<tests>
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<test>
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<param name="input" value="4.bed"/>
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<param name="size" value="5000"/>
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<param name="choice" value="1"/>
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<param name="offset" value="4000"/>
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<output name="out_file1" file="4_windows.bed"/>
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</test>
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</tests>
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<help>
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.. class:: infomark
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**What it does**
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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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-----
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.. class:: warningmark
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**Note**
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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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-----
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.. class:: infomark
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**About formats**
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**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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The first three BED fields (required) are::
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1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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The additional BED fields (optional) are::
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4. name - The name of the BED line.
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5. score - A score between 0 and 1000.
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6. strand - Defines the strand - either '+' or '-'.
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7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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9. reserved - This should always be set to zero.
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10. blockCount - The number of blocks (exons) in the BED line.
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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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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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13. expCount - The number of experiments.
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14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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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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-----
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**Example**
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- For the following query::
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chr22 1000 4700 NM_174568 0 +
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- running this tool with **Window size as 1000**, will return::
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chr22 1000 2000 NM_174568 0 +
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chr22 2000 3000 NM_174568 0 +
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chr22 3000 4000 NM_174568 0 +
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- running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
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chr22 1000 2000 NM_174568 0 +
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chr22 1500 2500 NM_174568 0 +
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chr22 2000 3000 NM_174568 0 +
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chr22 2500 3500 NM_174568 0 +
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chr22 3000 4000 NM_174568 0 +
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chr22 3500 4500 NM_174568 0 +
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</help>
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</tool> |