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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
author devteam
date Mon, 13 Jun 2022 16:26:51 +0000
parents 37652c34b3bf
children
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d00c8ea7792c Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_basecoverage_1" name="Base Coverage" version="1.0.0">
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37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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2 <description>of all intervals</description>
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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3 <macros>
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devteam
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4 <import>macros.xml</import>
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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5 </macros>
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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6 <expand macro="requirements" />
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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7 <code file="operation_filter.py"/>
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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8 <command><![CDATA[
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9 python '$__tool_directory__/gops_basecoverage.py'
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 '$input1'
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11 '$output'
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13 ]]></command>
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14 <inputs>
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15 <param name="input1" type="data" format="interval" label="Compute coverage for" />
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="txt" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="1.bed" />
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 <output name="output" file="gops_basecoverage_out.txt" />
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24 </test>
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devteam
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25 <test>
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26 <param name="input1" value="gops_bigint.interval" />
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 <output name="output" file="gops_basecoverage_out2.txt" />
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28 </test>
37652c34b3bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 </tests>
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30 <help><![CDATA[
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31 .. class:: infomark
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32
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33 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
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34
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35 This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total.
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36
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37 @SCREENCASTS@
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38
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39 **Example**
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40
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41 .. image:: gops_baseCoverage.gif
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42 ]]></help>
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43 </tool>