Mercurial > repos > mvdbeek > zerone_damid

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planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
author mvdbeek
date Fri, 14 Sep 2018 04:52:55 -0400
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7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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1 <tool id="zerone_damid" name="Discretize DamID experiments with Zerone" version="1.0">
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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2 <requirements>
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3 <requirement type="package" version="1.0">r-zerone</requirement>
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4 <requirement type="package" version="2.9.3">rpy2</requirement>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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5 <requirement type="package" version="0.23">pandas</requirement>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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6 <requirement type="package" version="6.7">click</requirement>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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7 </requirements>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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8 <command detect_errors="exit_code"><![CDATA[
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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9 python '$__tool_directory__/r-zerone.py'
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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10 #for c in $control_files:
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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11 --control_files '$c'
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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12 #end for
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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13 #for d in $fusion_files:
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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14 --fusion_files '$d'
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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15 #end for
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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16 --output '$output'
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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17 ]]></command>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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18 <inputs>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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19 <param argument="--control_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID control" help="You can produce these files uing bedtools coverageBed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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20 <param argument="--fusion_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID fusion" help="You can produce these files uing bedtools coverageBed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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21 </inputs>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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22 <outputs>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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23 <data name="output" label="Discretized DamID profile for ${on_string}" format="bed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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24 </outputs>
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25 <tests>
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26 <test>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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27 <param name="control_files" value="c1.bed,c2.bed" ftype="bed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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28 <param name="damid_files" value="d1.bed,d2.bed" ftype="bed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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29 <output name="output" value="discrete.bed" ftype="bed"/>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
mvdbeek
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30 </test>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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31 </tests>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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32 <help><![CDATA[
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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33
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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34 Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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35
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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36 This wrapper uses the zerone R package to discretize quantified GATC counts.
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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37 ]]></help>
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38 <citations>
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39 <citation type="doi">10.1093/bioinformatics/btw336</citation>
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40 </citations>
7fbff19b4485 planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
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41 </tool>