annotate galaxy-conf/GaussianSmooth.xml @ 12:81d5b81fb3c2 draft

Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
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children 3e477c7e0e73
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1 <tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
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6 <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" />
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7 </inputs>
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8 <outputs>
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9 <data format="wig" name="output" metadata_source="input" />
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10 </outputs>
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11 <tests>
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12 <!--<test>
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13 <param name="input" value="test.wig"/>
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14 <param name="dbkey" value="sacCer2"/>
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15 <param name="S" value="20"/>
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16 <param name="W" value="3"/>
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17 <output name="output" file="smoother.output1"/>
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18 </test>
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19 <test>
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20 <param name="input" value="test.bw"/>
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21 <param name="dbkey" value="sacCer2"/>
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22 <param name="S" value="20"/>
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23 <param name="W" value="3"/>
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24 <output name="output" file="smoother.output1"/>
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25 </test>
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26 <test>
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27 <param name="input" value="test.wig"/>
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28 <param name="dbkey" value="sacCer2"/>
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29 <param name="S" value="10"/>
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30 <param name="W" value="2"/>
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31 <output name="output" file="smoother.output2"/>
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32 </test>
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33 <test>
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34 <param name="input" value="test.bw"/>
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35 <param name="dbkey" value="sacCer2"/>
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36 <param name="S" value="10"/>
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37 <param name="W" value="2"/>
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38 <output name="output" file="smoother.output2"/>
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39 </test>
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40 <test>
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41 <param name="input" value="test.wig"/>
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42 <param name="dbkey" value="sacCer2"/>
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43 <param name="S" value="50"/>
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44 <param name="W" value="1"/>
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45 <output name="output" file="smoother.output3"/>
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46 </test>
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47 <test>
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48 <param name="input" value="test.bw"/>
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49 <param name="dbkey" value="sacCer2"/>
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50 <param name="S" value="5"/>
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51 <param name="W" value="1"/>
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52 <output name="output" file="smoother.output3"/>
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53 </test>-->
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54 </tests>
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55
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56 <help>
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57
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58 This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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59
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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60 .. _Gaussian: http://en.wikipedia.org/wiki/Gaussian_filter
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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61
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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62 .. class:: infomark
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63
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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64 **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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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66 </help>
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67 </tool>