Mercurial > repos > bgruening > music_inspect_eset

comparison inspect_eset.xml @ 2:577435e5e6b2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
author bgruening
date Sat, 29 Jan 2022 12:51:27 +0000
parents 817eb707bbf4
children 7705cc75ac18
comparison
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1:817eb707bbf4 2:577435e5e6b2
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf' 9 Rscript --vanilla '$conf'
10 ]]></command> 10 ]]></command>
11 <configfiles> 11 <configfiles>
12 <configfile name="conf" > 12 <configfile name="conf" >
13 13
14 null_str_vec = function(gstr){ 14 null_str_vec = function(gstr){
24 24
25 rds_eset = readRDS('$rds_eset') 25 rds_eset = readRDS('$rds_eset')
26 inspector = null_str_vec('$inspector') 26 inspector = null_str_vec('$inspector')
27 outfile_tab='$out_tab' 27 outfile_tab='$out_tab'
28 28
29 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
30 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
31
32 printout = function(text) {
33 if (typeof(text) %in% c("list", "vector", "integer", "double", "numeric")) {
34 write.table(text, file = outfile_tab, quote = F, sep = "\t",
35 col.names = NA)
36 } else {
37 ## text
38 print(typeof(text))
39 capture.output(text, file = outfile_tab) # nolint
40 }
41 }
42
43 if (inspector %in% c("print", "pData", "fData", "dims",
44 "experimentData", "protocolData", "exprs",
45 "signature", "annotation", "abstract")) {
46 op = get(inspector)
47 tab = op(rds_eset)
48 printout(tab)
49 } else {
50 stop(paste0("No such option:", inspector))
51 }
52
53
29 </configfile> 54 </configfile>
30 </configfiles> 55 </configfiles>
31 <inputs> 56 <inputs>
32 <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" /> 57 <param name="rds_eset" label="ESet Dataset" type="data" format="@RDATATYPE@" />
33 <param name="inspector" label="Inspect" type="select" 58 <param name="inspector" label="Inspect" type="select"
34 help="Inspect an aspect of the ESet dataset" > 59 help="Inspect an aspect of the ESet dataset" >
35 <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet --> 60 <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
36 <option value="print" selected="true">General Information</option> 61 <option value="print" selected="true">General Information</option>
37 <option value="exprs" >Expression Data Table</option> 62 <option value="exprs" >Expression Data Table</option>