Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Downsample.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents eb53be9a09f4
children
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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1 <tool id="WigDownsample" name="Downsample" version="1.1.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="Original data" />
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6 <param name="window" type="integer" value="100" label="Window size (bp)" />
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7 <param name="metric" type="select" label="Downsampling method">
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8 <option value="mean">Mean</option>
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9 <option value="min">Minimum</option>
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10 <option value="max">Maximum</option>
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11 <option value="coverage">Coverage</option>
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12 <option value="total">Total</option>
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="wig" name="output" metadata_source="input" />
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17 </outputs>
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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19 <tests>
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20 <test>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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21 <param name="input" value="wigmath1.wig"/>
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22 <param name="window" value="1"/>
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23 <param name="metric" value="mean"/>
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24 <output name="output" file="downsample1.wig"/>
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25 </test>
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26 <test>
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27 <param name="input" value="wigmath2.bw"/>
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28 <param name="window" value="5"/>
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29 <param name="metric" value="max"/>
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30 <output name="output" file="downsample2.wig"/>
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31 </test>
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32 <test>
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33 <param name="input" value="wigmath3.wig"/>
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34 <param name="window" value="100"/>
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35 <param name="metric" value="total"/>
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36 <output name="output" file="downsample3.wig"/>
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37 </test>
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38 </tests>
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39
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40 <help>
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41
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42 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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44 -----
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45
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46 **Downsampling Methods**
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47
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48 - **Mean:** the arithmetic mean of the values in the original data window
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49 - **Minimum:** the least value in the original data window
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50 - **Maximum:** the greatest value in the original data window
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51 - **Coverage:** the fraction of bases with values in the original window
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52 - **Total:** the sum of all values in the original data window
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53
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54 -----
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56 .. class:: infomark
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58 **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.
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60 </help>
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61 </tool>