Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Divide.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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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="WigDivide" name="Divide" version="1.1.0">
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2 <description>two (Big)Wig files</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Divide -n $dividend -d $divisor -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="dividend" type="data" label="File 1 (dividend)" />
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6 <param format="bigwig,wig" name="divisor" type="data" label="File 2 (divisor)" />
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7 </inputs>
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8 <outputs>
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9 <data format="wig" name="output" metadata_source="dividend" />
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10 </outputs>
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11 <tests>
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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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12 <test>
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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13 <param name="dividend" value="wigmath1.wig"/>
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
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14 <param name="divisor" value="wigmath2.wig"/>
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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15 <output name="output" file="divide1.wig"/>
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16 </test>
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17 <test>
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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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18 <param name="dividend" value="wigmath1.wig"/>
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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19 <param name="divisor" value="wigmath3.bw"/>
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20 <output name="output" file="divide2.wig"/>
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21 </test>
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22 <test>
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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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23 <param name="dividend" value="wigmath3.bw"/>
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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24 <param name="divisor" value="wigmath2.bw"/>
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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25 <output name="output" file="divide3.wig"/>
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26 </test>
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27 </tests>
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28
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29 <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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31 .. class:: infomark
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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33 **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.
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34
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35 </help>
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36 </tool>