Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/StripMatrix.xml @ 16:35031c567ece draft

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Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
author timpalpant
date Sat, 09 Jun 2012 16:06:25 -0400
parents 3e477c7e0e73
children
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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.
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1 <tool id="StripMatrix" name="Strip headers" version="1.1.0">
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2 <description>from an aligned matrix</description>
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3 <command interpreter="sh">galaxyToolRunner.sh visualization.StripMatrix -i $input -o $output</command>
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4 <inputs>
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5 <param format="tabular" name="input" type="data" label="Aligned matrix" />
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6 </inputs>
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7 <outputs>
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8 <data format="tabular" name="output" metadata="input" />
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input" value="test.matrix2png.txt"/>
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13 <output name="output" file="stripMatrix.txt"/>
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14 </test>
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15 </tests>
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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 This tool is intended to strip the column/row headers off of an aligned matrix (in matrix2png format) for easy import into Matlab or other software where only the data values are required. It removes the first row and first column from a tabular file.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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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21 -----
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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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23 **Example**
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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 If the following tabular matrix is used as input ::
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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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27 ID col1 col2 col3
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28 row1 2 4 5
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29 row2 5 1 1
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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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31 then the following tabular matrix will be produced as output ::
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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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33 2 4 5
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34 5 1 1
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36 </help>
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37 </tool>