Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/ZScore.xml @ 25:b43c420a6135 draft default tip
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
| author | timpalpant |
|---|---|
| date | Sat, 09 Feb 2019 14:02:24 -0500 |
| parents | a77e126ae856 |
| children |
| rev | line source |
|---|---|
| 24 | 1 <tool id="WigZScore" name="Z-Score" version="1.2.0"> |
| 2 <description>a (Big)Wig file</description> | |
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b43c420a6135
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
timpalpant
parents:
24
diff
changeset
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3 <command interpreter="bash">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command> |
| 24 | 4 <inputs> |
| 5 <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" /> | |
| 6 <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Z-score chromosomes individually" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="wig" name="output" metadata_source="input" /> | |
| 10 </outputs> | |
| 11 <tests> | |
| 12 <test> | |
| 13 <param name="input" value="wigmath1.wig"/> | |
| 14 <output name="output" file="zscorer1.wig"/> | |
| 15 </test> | |
| 16 <test> | |
| 17 <param name="input" value="wigmath2.wig"/> | |
| 18 <output name="output" file="zscorer2.wig"/> | |
| 19 </test> | |
| 20 <test> | |
| 21 <param name="input" value="wigmath3.wig"/> | |
| 22 <output name="output" file="zscorer3.wig"/> | |
| 23 </test> | |
| 24 <test> | |
| 25 <param name="input" value="wigmath1.bw"/> | |
| 26 <output name="output" file="zscorer4.wig"/> | |
| 27 </test> | |
| 28 <test> | |
| 29 <param name="input" value="wigmath2.bw"/> | |
| 30 <output name="output" file="zscorer5.wig"/> | |
| 31 </test> | |
| 32 <test> | |
| 33 <param name="input" value="wigmath3.bw"/> | |
| 34 <output name="output" file="zscorer6.wig"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 | |
| 38 <help> | |
| 39 | |
| 40 This tool will compute normal scores (Z-scores) for each of the values in a Wig file. For each base pair, the Z-scored value is equal to the deviance from the mean divided by the standard deviation (i.e. the number of standard deviations a value is away from the mean). The output file should have mean 0 and standard deviation 1. | |
| 41 | |
| 42 .. class:: infomark | |
| 43 | |
| 44 This tool is equivalent to using the **Mean Shift** tool to shift a Wig file to mean 0, then using the **Scale** tool to scale by 1/(standard deviation). | |
| 45 | |
| 46 .. class:: infomark | |
| 47 | |
| 48 **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. | |
| 49 | |
| 50 </help> | |
| 51 </tool> |