Mercurial > repos > devteam > windowsplitter
annotate windowSplitter.xml @ 1:477a0cfe6e6c
Corrected version string.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Thu, 10 Apr 2014 13:47:14 -0400 |
| parents | 4815516900d4 |
| children | 1fb384fb950e |
| rev | line source |
|---|---|
|
1
477a0cfe6e6c
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
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1 <tool id="winSplitter" name="Make windows" version="1.0.0"> |
| 0 | 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 | |
| 39 This 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 | |
| 47 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. | |
| 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 | |
| 57 The 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 | |
| 63 The 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> |