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author kyost
date Fri, 04 May 2018 02:24:47 -0400
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1 <tool id="make_window_bed" name="Create bed file of qPCR windows" version="0.1.0">
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2 <description> Creates bed file of windows spanning peaks of interest.</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__/make_window_bed.R $input1 $input2 $output
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="bed" label="Peak Bed File"/>
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11 <param type="integer" name="input2" value="100" label="Window Size"/>
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12 </inputs>
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13 <outputs>
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14 <data name="output" format="bed" label="qPCR Window Bed File"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input1" value="RAMA_peaks.bed"/>
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19 <param name="input2" value="100"/>
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20 <output name="output" file="qPCR_windows.bed"/>
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21 </test>
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22 </tests>
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23 <help><![CDATA[
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24 Generates bed file containing overlapping windows of specified size spanning peaks in input bed file.
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25 ]]></help>
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26 <citations>
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27 <citation type="doi">doi:10.1038/nmeth.4663</citation>
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28 </citations>
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29 </tool>