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comparison inspect_eset.xml @ 0:2fed32b5aa02 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
author bgruening
date Sun, 12 Sep 2021 19:48:26 +0000
parents
children 817eb707bbf4
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-1:000000000000 0:2fed32b5aa02
1 <tool id="music_inspect_eset" name="Inspect Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="20.05" license="GPL-3.0-or-later" >
3 <description>Inspect an ExpressionSet object by a variety of attributes</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf'
10 ]]></command>
11 <configfiles>
12 <configfile name="conf" >
13
14 null_str_vec = function(gstr){
15 tokens = unlist(as.vector(strsplit(gstr, split=",")))
16 if (length(tokens) == 0){
17 return(NULL)
18 }
19 if (length(tokens) == 1){
20 return(tokens[[1]])
21 }
22 return(tokens)
23 }
24
25 rds_eset = readRDS('$rds_eset')
26 inspector = null_str_vec('$inspector')
27 outfile_tab='$out_tab'
28
29 </configfile>
30 </configfiles>
31 <inputs>
32 <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" />
33 <param name="inspector" label="Inspect" type="select"
34 help="Inspect an aspect of the ESet dataset" >
35 <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
36 <option value="print" selected="true">General Information</option>
37 <option value="exprs" >Expression Data Table</option>
38 <option value="pData" >PhenoType Data Table</option>
39 <option value="fData" >Feature Data Table</option>
40 <option value="dims" >Dimension</option>
41 <option value="experimentData" />
42 <option value="signature" />
43 <option value="annotation" />
44 <option value="abstract" />
45 </param>
46 </inputs>
47 <outputs>
48 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result" />
49 </outputs>
50 <tests>
51 <test expect_num_outputs="1" >
52 <!-- Inspect 0 -->
53 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
54 <param name="inspector" value="print" />
55 <output name="out_tab" >
56 <assert_contents>
57 <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
58 </assert_contents>
59 </output>
60 </test>
61 <test expect_num_outputs="1" >
62 <!-- Inspect 1 -->
63 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
64 <param name="inspector" value="pData" />
65 <output name="out_tab" >
66 <assert_contents>
67 <has_n_columns n="5" />
68 <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
69 </assert_contents>
70 </output>
71 </test>
72 <test expect_num_outputs="1" >
73 <!-- Inspect 2 -->
74 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
75 <param name="inspector" value="dims" />
76 <output name="out_tab" >
77 <assert_contents>
78 <has_n_columns n="1" />
79 <has_text_matching expression="Samples\s+\d{1,4}"/>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help><![CDATA[
85 Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations.
86
87 For more options and information, consult `the manual <http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf>`_ and the `rdocumentation <https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet>`_
88 .
89 ]]></help>
90 <citations>
91 <citation type="bibtex">
92 @misc{falcon2007introduction,
93 title={An introduction to bioconductor’s expressionset class},
94 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
95 year={2007}
96 }
97 </citation>
98 </citations>
99 </tool>