Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Downsample.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
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children eb53be9a09f4
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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1 <tool id="WigDownsample" name="Downsample" version="1.0.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
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4 <inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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5 <param format="bigwig,wig" name="input" type="data" label="Original data" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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6 <param name="window" type="integer" value="100" label="Window size (bp)" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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7 <param name="metric" type="select" label="Downsampling method">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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8 <option value="mean">Mean</option>
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9 <option value="min">Min</option>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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10 <option value="max">Max</option>
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11 </param>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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12 </inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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13 <outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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14 <data format="wig" name="output" metadata_source="input" />
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15 </outputs>
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17 <help>
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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19 .. class:: infomark
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20
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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21 **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.
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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.
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25 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping moving windows starting from the beginning of each chromosome. Each window can be downsampled as the arithmetic mean, minimum, or maximum value of the original data.
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27 </help>
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28 </tool>