Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/GaussianSmooth.xml @ 14:f58706d4d421 draft
Uploaded
| author | timpalpant |
|---|---|
| date | Sat, 19 May 2012 10:40:16 -0400 |
| parents | 81d5b81fb3c2 |
| children | 3e477c7e0e73 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0"> |
| 2 <description>a (Big)Wig file</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" /> | |
| 6 <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian 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:
4
diff
changeset
|
57 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
58 This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
59 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
60 .. _Gaussian: http://en.wikipedia.org/wiki/Gaussian_filter |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
61 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
62 .. class:: infomark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
63 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
64 **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:
4
diff
changeset
|
65 |
| 4 | 66 </help> |
| 67 </tool> |