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author kyost
date Fri, 04 May 2018 02:24:47 -0400
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fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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1 <tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0">
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2 <description> Determines optimal regions for designing ATAC-qPCR primers.</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.2" >r-base</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="tabular" label="Coverage Bed File"/>
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11 <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/>
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12 <param type="data" name="input3" format="tabular" label="Total Read Counts"/>
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13 <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/>
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14 <param type="integer" name="input5" value="3" label="Coverage Cutoff"/>
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15 </inputs>
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16 <outputs>
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17 <data name="output" format="bed" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input1" value="combined.o.bed.coverage"/>
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22 <param name="input2" value="combined.f9.bed.coverage"/>
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23 <param name="input3" value="lib_sizes.txt"/>
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24 <param name="input4" value="0.7"/>
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25 <param name="input5" value="2"/>
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26 <output name="output" file="qPCR_regions.bed"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height.
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31 ]]></help>
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32 <citations>
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33 <citation type="doi">doi:10.1038/nmeth.4663</citation>
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34 </citations>
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35 </tool>