Mercurial > repos > kyost > atac_primer_tool
annotate find_qPCR_regions.xml @ 2:6f5ce4e865a5 draft
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author | kyost |
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date | Sat, 28 Apr 2018 19:45:57 -0400 |
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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> |