Mercurial > repos > proteore > proteore_prot_features
changeset 5:867d47ff782c draft
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
| author | proteore |
|---|---|
| date | Wed, 14 Mar 2018 12:04:32 -0400 |
| parents | bbb17bca9ec1 |
| children | fc0118aa432a |
| files | README.rst prot_features.xml protein_features.R |
| diffstat | 3 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/README.rst Thu Mar 08 10:47:00 2018 -0500 +++ b/README.rst Wed Mar 14 12:04:32 2018 -0400 @@ -21,8 +21,8 @@ **Databases** -Annotations have been retrieved from the neXtProt database (Gaudet et al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) +Annotations have been retrieved from the neXtProt database released on 01/08/2017 (Gaudet et al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) **Outputs** -The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected. \ No newline at end of file +The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.
--- a/prot_features.xml Thu Mar 08 10:47:00 2018 -0500 +++ b/prot_features.xml Wed Mar 14 12:04:32 2018 -0400 @@ -123,7 +123,7 @@ **Databases** -Annotations have been retrieved from the neXtProt database (Gaudet et al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) +Annotations have been retrieved from the neXtProt database released on 01/08/2017 (Gaudet et al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) **Outputs**
--- a/protein_features.R Thu Mar 08 10:47:00 2018 -0500 +++ b/protein_features.R Wed Mar 14 12:04:32 2018 -0400 @@ -70,8 +70,12 @@ input = c(input, strsplit(row, ";")[[1]][1]) } } + + # Read reference file nextprot_file = args$nextprot - nextprot = human_id_map = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "") + nextprot = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "") + + # Parse arguments typeid = args$type P1_args = strsplit(args$argsP1, ",")[[1]] P2_args = strsplit(args$argsP2, ",")[[1]] @@ -130,4 +134,4 @@ } } -protein_features() \ No newline at end of file +protein_features()