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planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
author kpbioteam
date Sun, 11 Feb 2018 07:35:45 -0500
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
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1 <tool id="minfi_ppquantile" name="minfi_ppquantile" version="0.1.0">
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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2 <description>implements stratified quantile normalization preprocessing</description>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
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3 <requirements>
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kpbioteam
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4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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5 <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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6 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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7 </requirements>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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8 <command detect_errors="exit_code"><![CDATA[
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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9 Rscript ${__tool_directory__}/minfi_ppquantile.R "$input1" "$output1"
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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10 ]]></command>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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11 <inputs>
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kpbioteam
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12 <param type="data" name="input1" format="rdata" />
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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13 </inputs>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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14 <outputs>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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15 <data name="output1" format="rdata" />
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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16 </outputs>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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17 <tests>
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kpbioteam
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18 <test>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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19 <param name="input1" value="RGSet.rdata"/>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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20 <output name="output1" file="quantile.rdata"/>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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21 </test>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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22 </tests>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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23 <help><![CDATA[
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
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24 The normalization procedure is applied to the Meth and Unmeth intensities separately. The distribution of type I and type II signals is forced to be the same by first quantile normalizing the type II probes across samples and then interpolating a reference distribution to which we normalize the type I probes. Since probe types and probe regions are confounded and we know that DNAm distributions vary across regions we stratify the probes by region before applying this interpolation.
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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25 ]]></help>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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26 <citations>
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kpbioteam
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27 <citation type="doi">10.1093/bioinformatics/btu049</citation>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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28 </citations>
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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29 </tool>