Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/Phasogram.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 |
|---|---|
| 4 | 1 <tool id="Phasogram" name="Make phasogram" version="1.0.0"> |
| 2 <description>of dyads</description> | |
| 5 | 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command> |
| 4 | 4 <inputs> |
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4fc118372ae7
Uploaded new version with fixes and broader support for interval files
timpalpant
parents:
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diff
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5 <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" /> |
| 4 | 6 <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" /> |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data name="output" format="tabular" /> | |
| 10 </outputs> | |
| 11 | |
| 12 <help> | |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
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13 |
| 13 | 14 This tool calculates the phase distribution of sequencing data. It can be used to identify genome-wide periodicities. Phase counts are aggregated for each base pair across the genome. This is equivalent to summing the autocovariance of a sliding window across the genome. The tool is a reimplementation of the algorithm described in (Valouev et al. 2011). |
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12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
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15 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
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16 .. class:: infomark |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
17 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
18 **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:
7
diff
changeset
|
19 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
20 ----- |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
21 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
22 **Citation** |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
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23 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
24 Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ and Sidow A (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516–520 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
7
diff
changeset
|
25 |
| 4 | 26 </help> |
| 27 </tool> |