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annotate minfi_ppnoob.xml @ 0:a003221d59cc draft default tip

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planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
author kpbioteam
date Sun, 11 Feb 2018 08:28:49 -0500
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a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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1 <tool id="minfi_ppnoob" name="minfi_ppnoob" version="0.1.0">
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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2 <description>implements the noob background subtraction method with dye-bias normalization</description>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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3 <requirements>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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5 <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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6 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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7 </requirements>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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8 <command detect_errors="exit_code"><![CDATA[
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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9 Rscript ${__tool_directory__}/minfi_ppnoob.R "$input1" "$output1"
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
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10 ]]></command>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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11 <inputs>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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12 <param type="data" name="input1" format="rdata" />
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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13 </inputs>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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14 <outputs>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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15 <data name="output1" format="rdata" />
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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16 </outputs>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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17 <tests>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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18 <test>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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19 <param name="input1" value="RGSet.rdata"/>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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20 <output name="output1" file="noob.rdata"/>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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21 </test>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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22 </tests>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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23 <help><![CDATA[
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
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24 Background subtraction method estimates background noise from the out-of-band probes and remove it for each sample separately, while the dye-bias normalization utilizes a subset of the control probes to estimate the dye bias.
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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25 ]]></help>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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26 <citations>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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27 <citation type="doi">10.1093/bioinformatics/btu049</citation>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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28 </citations>
a003221d59cc planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
kpbioteam
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29 </tool>