Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/MovingAverageSmooth.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 | 81d5b81fb3c2 |
| 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:
12
diff
changeset
|
1 <tool id="WigMovingAverage" name="Moving average smooth" version="1.1.0"> |
| 4 | 2 <description>a (Big)Wig file</description> |
| 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" /> | |
| 6 <param name="W" type="integer" value="20" optional="true" label="Width of the moving average in base pairs" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="wig" name="output" metadata_source="input" /> | |
| 10 </outputs> | |
| 11 <tests> | |
| 12 <!--<test> | |
| 13 <param name="input" value="test.wig"/> | |
| 14 <param name="dbkey" value="sacCer2"/> | |
| 15 <param name="S" value="20"/> | |
| 16 <param name="W" value="3"/> | |
| 17 <output name="output" file="smoother.output1"/> | |
| 18 </test> | |
| 19 <test> | |
| 20 <param name="input" value="test.bw"/> | |
| 21 <param name="dbkey" value="sacCer2"/> | |
| 22 <param name="S" value="20"/> | |
| 23 <param name="W" value="3"/> | |
| 24 <output name="output" file="smoother.output1"/> | |
| 25 </test> | |
| 26 <test> | |
| 27 <param name="input" value="test.wig"/> | |
| 28 <param name="dbkey" value="sacCer2"/> | |
| 29 <param name="S" value="10"/> | |
| 30 <param name="W" value="2"/> | |
| 31 <output name="output" file="smoother.output2"/> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="input" value="test.bw"/> | |
| 35 <param name="dbkey" value="sacCer2"/> | |
| 36 <param name="S" value="10"/> | |
| 37 <param name="W" value="2"/> | |
| 38 <output name="output" file="smoother.output2"/> | |
| 39 </test> | |
| 40 <test> | |
| 41 <param name="input" value="test.wig"/> | |
| 42 <param name="dbkey" value="sacCer2"/> | |
| 43 <param name="S" value="50"/> | |
| 44 <param name="W" value="1"/> | |
| 45 <output name="output" file="smoother.output3"/> | |
| 46 </test> | |
| 47 <test> | |
| 48 <param name="input" value="test.bw"/> | |
| 49 <param name="dbkey" value="sacCer2"/> | |
| 50 <param name="S" value="5"/> | |
| 51 <param name="W" value="1"/> | |
| 52 <output name="output" file="smoother.output3"/> | |
| 53 </test>--> | |
| 54 </tests> | |
| 55 | |
| 56 <help> | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
57 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
58 This tool smooths genomic data with a mean_ filter of the specified width. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
59 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
60 .. _mean: http://en.wikipedia.org/wiki/Moving_average |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
61 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
62 .. class:: warningmark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
63 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
64 Note that for the moving average to be perfectly symmetric, the window should be an odd number of base pairs. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
65 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
66 .. 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
|
67 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
69 |
| 4 | 70 </help> |
| 71 </tool> |