Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/ZScore.xml @ 15:3e477c7e0e73 draft
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 |
| rev | line source |
|---|---|
|
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.
timpalpant
parents:
13
diff
changeset
|
1 <tool id="WigZScore" name="Z-Score" version="1.2.0"> |
| 4 | 2 <description>a (Big)Wig file</description> |
|
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.
timpalpant
parents:
13
diff
changeset
|
3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command> |
| 4 | 4 <inputs> |
| 5 <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" /> | |
|
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.
timpalpant
parents:
13
diff
changeset
|
6 <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Z-score chromosomes individually" /> |
| 4 | 7 </inputs> |
| 8 <outputs> | |
| 9 <data format="wig" name="output" metadata_source="input" /> | |
| 10 </outputs> | |
| 11 <tests> | |
| 13 | 12 <test> |
| 13 <param name="input" value="wigmath1.wig"/> | |
| 14 <output name="output" file="zscorer1.wig"/> | |
| 4 | 15 </test> |
| 16 <test> | |
| 13 | 17 <param name="input" value="wigmath2.wig"/> |
| 18 <output name="output" file="zscorer2.wig"/> | |
| 4 | 19 </test> |
| 20 <test> | |
| 13 | 21 <param name="input" value="wigmath3.wig"/> |
| 22 <output name="output" file="zscorer3.wig"/> | |
| 4 | 23 </test> |
| 24 <test> | |
| 13 | 25 <param name="input" value="wigmath1.bw"/> |
| 26 <output name="output" file="zscorer4.wig"/> | |
| 4 | 27 </test> |
| 28 <test> | |
| 13 | 29 <param name="input" value="wigmath2.bw"/> |
| 30 <output name="output" file="zscorer5.wig"/> | |
| 4 | 31 </test> |
| 32 <test> | |
| 13 | 33 <param name="input" value="wigmath3.bw"/> |
| 34 <output name="output" file="zscorer6.wig"/> | |
| 35 </test> | |
| 4 | 36 </tests> |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
37 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
38 <help> |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
39 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
41 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
42 .. class:: infomark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
43 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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). |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
45 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
46 .. class:: infomark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
47 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
49 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
50 </help> |
| 4 | 51 </tool> |