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comparison galaxy-conf/Scale.xml @ 15:3e477c7e0e73 draft

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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
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14:f58706d4d421 15:3e477c7e0e73
1 <tool id="WigScale" name="Scale" version="1.0.0"> 1 <tool id="WigScale" name="Scale" version="1.2.0">
2 <description>a (Big)Wig file</description> 2 <description>a (Big)Wig file</description>
3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command>
4 <inputs> 4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Scale the data in" /> 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)" /> 6 <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" />
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)" />
7 </inputs> 8 </inputs>
8 <outputs> 9 <outputs>
9 <data format="wig" name="output" metadata_source="input" /> 10 <data format="wig" name="output" metadata_source="input" />
10 </outputs> 11 </outputs>
11 <tests> 12 <tests>
47 </test>--> 48 </test>-->
48 </tests> 49 </tests>
49 50
50 <help> 51 <help>
51 52
52 This tool will multiply all values in a Wig file by a scalar. 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. 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.
53 54
54 .. class:: infomark 55 .. class:: infomark
55 56
56 **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. 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.
57 58