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1 <tool id="countsAroundTSS" name="None" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <command detect_errors="exit_code"><![CDATA[
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5 Rscript countsAroundTSS.R --input $bam --input $genome --input $up_stream --input $downstream --input $TxDb --output $output
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6 ]]></command>
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7 <inputs>
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8 <param type="data" name="bam" format="" />
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9 <param type="data" name="genome" type="character" />
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10 <param type="data" name="up_stream" type="integer" />
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11 <param type="data" name="downstream" type="integer" />
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12 <param type="data" name="TxDb" optional="true" format="sqlite" />
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13 </inputs>
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14 <outputs>
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15 <data name="ENCFF027UTM" format="txt" />
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16 </outputs>
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17 <help><![CDATA[
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18 TODO: Fill in help.
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19 ]]></help>
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20 <citations>
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21 <citation type="bibtex">
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22 @misc{renameTODO,
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23 author = {LastTODO, FirstTODO},
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24 year = {TODO},
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25 title = {TODO},
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26 url = {https://www.cyberciti.biz/faq/list-the-contents-of-a-tar-or-targz-file/},
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27 }</citation>
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28 </citations>
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29 </tool>
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