Mercurial > repos > kpbioteam > ewastools
annotate minfi_rset.xml @ 76:fef50103f6b3 draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author | kpbioteam |
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date | Fri, 07 Jun 2019 08:57:26 -0400 |
parents | 9c6fbb7d5a2a |
children |
rev | line source |
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70 | 1 <tool id="minfi_rset" name="Minfi Rset" version="@MINFI_VERSION@"> |
4 | 2 <description>store Beta values and/or M values</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 Rscript '$read_rset_script' | |
10 ]]> | |
11 </command> | |
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9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
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12 <configfiles> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
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13 <configfile name="read_rset_script"> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
|
14 <![CDATA[ |
4 | 15 require("minfi", quietly = TRUE) |
16 MSet <- get(load('$mset')) | |
17 | |
18 RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE) | |
19 | |
20 save(RSet,file = '$rset') | |
21 ]]> </configfile> | |
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
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22 </configfiles> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
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23 <inputs> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
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24 <param type="data" name="mset" format="rdata" label="MethylSet" |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
70
diff
changeset
|
25 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> |
4 | 26 </inputs> |
27 <outputs> | |
28 <data name="rset" format="rdata" label="RatioSet"/> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="mset" value="MethylSet.rdata"/> | |
33 <output name="rset" file="RatioSet.rdata"/> | |
34 </test> | |
35 </tests> | |
36 <help><![CDATA[ | |
37 RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix. | |
38 ]]></help> | |
39 <expand macro="citations" /> | |
40 </tool> |