Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Summary.xml @ 18:b2a69d34385a draft

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Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
author timpalpant
date Fri, 15 Jun 2012 15:07:33 -0400
parents 3e477c7e0e73
children b43c420a6135
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15
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="WigSummary" name="Output a summary" version="1.1.0">
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2 <description>of a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
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6 </inputs>
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7 <outputs>
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8 <data format="txt" name="output" />
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input" value="wigmath1.wig"/>
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13 <output name="output" file="wigsummary1.txt"/>
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14 </test>
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15 <test>
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16 <param name="input" value="test.wig"/>
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17 <output name="output" file="wigsummary2.txt"/>
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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 <output name="output" file="wigsummary3.txt"/>
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22 </test>
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23 </tests>
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24
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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25 <help>
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26
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27 This tool will output a summary of a Wig or BigWig file, including information about the chromosomes and types of contigs in the Wig file, as well as basic descriptive statistics.
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28
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29 -----
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30
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31 **Example:**
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32
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33 The following is an example of the output of this tool ::
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34
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35 ASCII Text Wiggle file: track type=wiggle_0
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36 Chromosomes:
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37 2micron start=1 stop=6318
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38 chrVI start=1 stop=270148
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39 chrI start=1 stop=230208
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40 chrIII start=1 stop=316617
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41 chrXII start=1 stop=1078175
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42 chrXV start=1 stop=1091289
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43 chrXVI start=1 stop=948062
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44 chrII start=1 stop=813178
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45 chrVIII start=1 stop=562643
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46 chrX start=1 stop=745742
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47 chrXIII start=1 stop=924429
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48 chrV start=1 stop=576869
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49 chrXIV start=1 stop=784333
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50 chrIV start=1 stop=1531919
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51 chrXI start=1 stop=666454
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52 chrIX start=1 stop=439885
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53 chrM start=1 stop=85779
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54 chrVII start=1 stop=1090947
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55 Contigs:
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56 fixedStep chrom=2micron start=1 span=1 step=1
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57 fixedStep chrom=chrVI start=1 span=1 step=1
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58 fixedStep chrom=chrI start=1 span=1 step=1
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59 fixedStep chrom=chrIII start=1 span=1 step=1
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60 fixedStep chrom=chrXII start=1 span=1 step=1
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61 fixedStep chrom=chrXVI start=1 span=1 step=1
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62 fixedStep chrom=chrXV start=1 span=1 step=1
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63 fixedStep chrom=chrII start=1 span=1 step=1
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64 fixedStep chrom=chrVIII start=1 span=1 step=1
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65 fixedStep chrom=chrXIII start=1 span=1 step=1
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66 fixedStep chrom=chrX start=1 span=1 step=1
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67 fixedStep chrom=chrV start=1 span=1 step=1
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68 fixedStep chrom=chrXIV start=1 span=1 step=1
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69 fixedStep chrom=chrIV start=1 span=1 step=1
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70 fixedStep chrom=chrXI start=1 span=1 step=1
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71 fixedStep chrom=chrIX start=1 span=1 step=1
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72 fixedStep chrom=chrM start=1 span=1 step=1
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73 fixedStep chrom=chrVII start=1 span=1 step=1
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74 Basic Statistics:
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75 Mean: 1.000000164913575
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76 Standard Deviation: 1.8843731523620193
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77 Total: 1.2162997005843896E7
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78 Bases Covered: 12162995
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79 Min value: 0.0
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80 Max value: 277.98996
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81
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82 </help>
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83 </tool>