Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/Downsample.xml @ 13:eb53be9a09f4 draft

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
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12:81d5b81fb3c2 13:eb53be9a09f4
4 <inputs> 4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Original data" /> 5 <param format="bigwig,wig" name="input" type="data" label="Original data" />
6 <param name="window" type="integer" value="100" label="Window size (bp)" /> 6 <param name="window" type="integer" value="100" label="Window size (bp)" />
7 <param name="metric" type="select" label="Downsampling method"> 7 <param name="metric" type="select" label="Downsampling method">
8 <option value="mean">Mean</option> 8 <option value="mean">Mean</option>
9 <option value="min">Min</option> 9 <option value="min">Minimum</option>
10 <option value="max">Max</option> 10 <option value="max">Maximum</option>
11 <option value="coverage">Coverage</option>
12 <option value="total">Total</option>
11 </param> 13 </param>
12 </inputs> 14 </inputs>
13 <outputs> 15 <outputs>
14 <data format="wig" name="output" metadata_source="input" /> 16 <data format="wig" name="output" metadata_source="input" />
15 </outputs> 17 </outputs>
16 18
17 <help> 19 <help>
18 20
21 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping windows starting from the beginning of each chromosome. Each window can be downsampled as the mean, minimum, maximum, total, or coverage of the original data.
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23 -----
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25 **Downsampling Methods**
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27 - **Mean:** the arithmetic mean of the values in the original data window
28 - **Minimum:** the least value in the original data window
29 - **Maximum:** the greatest value in the original data window
30 - **Coverage:** the fraction of bases with values in the original window
31 - **Total:** the sum of all values in the original data window
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33 -----
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19 .. class:: infomark 35 .. class:: infomark
20 36
21 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly. 37 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
22 38
23 -----
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25 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping moving windows starting from the beginning of each chromosome. Each window can be downsampled as the arithmetic mean, minimum, or maximum value of the original data.
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27 </help> 39 </help>
28 </tool> 40 </tool>