Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/MovingAverageSmooth.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
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20
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1 <tool id="WigMovingAverage" name="Moving average smooth" version="1.1.0">
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2 <description>a (Big)Wig file</description>
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b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
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3 <command interpreter="bash">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -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="W" type="integer" value="20" optional="true" label="Width of the moving average 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 a mean_ filter of the specified width.
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59
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60 .. _mean: http://en.wikipedia.org/wiki/Moving_average
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61
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62 .. class:: warningmark
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63
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64 Note that for the moving average to be perfectly symmetric, the window should be an odd number of base pairs.
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65
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66 .. class:: infomark
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67
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68 **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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69
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70 </help>
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71 </tool>