Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/Scale.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 |
|---|---|
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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
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1 <tool id="WigScale" name="Scale" version="1.2.0"> |
| 4 | 2 <description>a (Big)Wig file</description> |
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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
|
3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command> |
| 4 | 4 <inputs> |
| 5 <param format="bigwig,wig" name="input" type="data" label="Scale the data in" /> | |
| 6 <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" /> | |
|
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
|
7 <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Scale chromosomes to 1/mean individually (no effect if scale factor is specified)" /> |
| 4 | 8 </inputs> |
| 9 <outputs> | |
| 10 <data format="wig" name="output" metadata_source="input" /> | |
| 11 </outputs> | |
| 12 <tests> | |
| 13 <!--<test> | |
| 14 <param name="input" value="wigmath.input1"/> | |
| 15 <param name="T" value="0"/> | |
| 16 <param name="dbkey" value="sacCer2"/> | |
| 17 <output name="output" file="percenter.output1"/> | |
| 18 </test> | |
| 19 <test> | |
| 20 <param name="input" value="wigmath.input1.bw"/> | |
| 21 <param name="T" value="0"/> | |
| 22 <param name="dbkey" value="sacCer2"/> | |
| 23 <output name="output" file="percenter.output1"/> | |
| 24 </test> | |
| 25 <test> | |
| 26 <param name="input" value="wigmath.input2"/> | |
| 27 <param name="T" value="2"/> | |
| 28 <param name="dbkey" value="sacCer2"/> | |
| 29 <output name="output" file="percenter.output2"/> | |
| 30 </test> | |
| 31 <test> | |
| 32 <param name="input" value="wigmath.input2.bw"/> | |
| 33 <param name="T" value="2"/> | |
| 34 <param name="dbkey" value="sacCer2"/> | |
| 35 <output name="output" file="percenter.output2"/> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input" value="wigmath.input3"/> | |
| 39 <param name="T" value="1000000"/> | |
| 40 <param name="dbkey" value="sacCer2"/> | |
| 41 <output name="output" file="percenter.output3"/> | |
| 42 </test> | |
| 43 <test> | |
| 44 <param name="input" value="wigmath.input3.bw"/> | |
| 45 <param name="T" value="1000000"/> | |
| 46 <param name="dbkey" value="sacCer2"/> | |
| 47 <output name="output" file="percenter.output3"/> | |
| 48 </test>--> | |
| 49 </tests> | |
| 50 | |
| 51 <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
|
52 |
|
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
|
53 This tool will multiply all values in a Wig file by a scale factor. For example, this can be used to normalize to read depth by multiplying by 1/(# reads). By default, the tool will scale to 1/(mean value), which is equivalent to dividing by coverage and multiplying by the size of the genome. The resulting output file should have mean 1. |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
54 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
55 .. 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
|
56 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
57 **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
|
58 |
| 4 | 59 </help> |
| 60 </tool> |