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comparison construct_eset.xml @ 0:2cfd0db49bbc 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 19:49:12 +0000
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children be91cb6f48e7
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-1:000000000000 0:2cfd0db49bbc
1 <tool id="music_construct_eset" name="Construct Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="20.05" license="GPL-3.0-or-later" >
3 <description>Create an ExpressionSet object from tabular and textual data</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript --vanilla '$conf'
10 ]]></command>
11 <configfiles>
12 <configfile name="conf" >
13
14 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
15 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
16
17 null_str_vec = function(gstr){
18 tokens = unlist(as.vector(strsplit(gstr, split=",")))
19 if (length(tokens) == 0){
20 return(NULL)
21 }
22 if (length(tokens) == 1){
23 return(tokens[[1]])
24 }
25 return(tokens)
26 }
27
28 ## Assay Data
29 ## F rows of features and S columns of samples
30 ## - This file is the only non-optional parameter
31 exprs_file = '$exprs_file'
32 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
33 row.names = 1, as.is = T))
34 ## Phenotype Data
35 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
36 pdata = NULL
37 #if '$pdata_file':
38 pdata_file = '$pdata_file'
39 pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
40 #end if
41 ## Annotation and Feature Data, or just a string for type of chip used
42 annotation = null_str_vec('$annotation')
43
44 if (all(rownames(pdata) != colnames(exprs))) {
45 stop("Number of Samples between phenotypes and assays are not the same")
46 }
47
48 ##metadata = data.frame(
49 ## labelDescription = c(
50 ## "Patient gender",
51 ## "Case/Control",
52 ## "Tumor progress"),
53 ## row.names = c("gender", "type", "score"))
54 metadata = as.data.frame(do.call(rbind, list(
55 #for i, row in enumerate($metadata):
56 #if i==0
57 list(ldesc='$row.label_desc', lname='$row.row_names')
58 #else
59 ,list(ldesc='$row.label_desc', lname='$row.row_names')
60 #end if
61 #end for
62 )))
63 metadata\$labelDescription = unlist(metadata\$ldesc)
64 rownames(metadata) = unlist(metadata\$lname)
65 metadata\$ldesc = NULL
66 metadata\$lname = NULL
67
68 if (nrow(metadata)==0) {
69 metadata = NULL
70 }
71
72 pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
73
74 ## Experiment Description -- using the MIAME object
75 experiment_data = new(
76 "MIAME",
77 name = null_str_vec('$expdata.name'),
78 lab = null_str_vec('$expdata.lab'),
79 contact = null_str_vec('$expdata.contact'),
80 title = null_str_vec('$expdata.title'),
81 abstract = null_str_vec('$expdata.abstract'),
82 url = null_str_vec('$expdata.url'),
83 other = list(
84 #for i, row in enumerate($expdata.other):
85 #if i==0
86 '$row.field' = null_str_vec('$row.comment')
87 #else
88 ,'$row.field' = null_str_vec('$row.comment')
89 #end if
90 #end for
91 ))
92
93 e_set = ExpressionSet(assayData = exprs,
94 phenoData = pheno_data,
95 experimentData = experiment_data,
96 annotation = annotation)
97
98 capture.output(print(e_set), file = '$out_tab')
99 saveRDS(e_set, file= '$out_rds')
100
101 </configfile>
102 </configfiles>
103 <inputs>
104 <param name="exprs_file" label="Assay Data" type="data" format="tabular,tsv"
105 help="F rows of features and S columns of samples. A Tab delimited file, with a header line and the first column has row names." />
106 <param name="pdata_file" label="Phenotype Data" type="data"
107 format="tabular,tsv" optional="true"
108 help="S rows of samples, and V columns of covariates (e.g. sex, age)" />
109 <param name="annotation" label="Annotation" type="text"
110 optional="true" help="A string detailing which chip was used" >
111 <expand macro="validator_text_and_urls" />
112 </param>
113 <repeat name="metadata" title="Meta Data" min="0" max="15" >
114 <!-- optional, so min=0 -->
115 <param name="row_names" label="Label" type="text" >
116 <expand macro="validator_text_and_urls" />
117 </param>
118 <param name="label_desc" label="Label Description" type="text" >
119 <expand macro="validator_text_and_urls" />
120 </param>
121 </repeat>
122 <section name="expdata" title="Experiment Data" >
123 <param name="name" label="Experimenter Name" type="text" value="" optional="true" >
124 <expand macro="validator_text_and_urls" />
125 </param>
126 <param name="lab" label="Lab" type="text" value="" optional="true" >
127 <expand macro="validator_text_and_urls" />
128 </param>
129 <param name="contact" label="Contact" type="text" value="" optional="true" >
130 <expand macro="validator_text_and_urls" />
131 </param>
132 <param name="title" label="Title" type="text" value="" optional="true" >
133 <expand macro="validator_text_and_urls" />
134 </param>
135 <param name="abstract" label="Abstract" type="text" value="" optional="true" >
136 <expand macro="validator_text_and_urls" />
137 </param>
138 <param name="url" label="URL" type="text" value="" optional="true" >
139 <expand macro="validator_text_and_urls" />
140 </param>
141 <repeat name="other" title="Other Fields" min="1">
142 <param name="field" label="FieldName" type="text" value="notes" >
143 <expand macro="validator_text_and_urls" />
144 </param>
145 <param name="comment" label="Comment" type="text" value="Created in Galaxy" >
146 <expand macro="validator_text_and_urls" />
147 </param>
148 </repeat>
149 </section>
150 </inputs>
151 <outputs>
152 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: General Info" />
153 <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
154 </outputs>
155 <tests>
156 <test expect_num_outputs="2" >
157 <!-- Values from the manual -->
158 <param name="exprs_file" value="array.tsv" />
159 <param name="pdata_file" value="pheno.tsv" />
160 <param name="annotation" value="hgu95av2" />
161 <repeat name="metadata" >
162 <param name="row_names" value="gender" />
163 <param name="label_desc" value="Patient gender" />
164 </repeat>
165 <repeat name="metadata" >
166 <param name="row_names" value="type" />
167 <param name="label_desc" value="Case/control status" />
168 </repeat>
169 <repeat name="metadata" >
170 <param name="row_names" value="score" />
171 <param name="label_desc" value="Tumor Progress on XYZ scale" />
172 </repeat>
173 <section name="expdata">
174 <param name="name" value="Pierre Fermat" />
175 <param name="lab" value="Francis Galton Lab" />
176 <param name="contact" value="pfermat@lab.not.exist" />
177 <param name="title" value="Smoking-Cancer Experiment" />
178 <param name="abstract" value="An example ExpressionSet" />
179 <param name="url" value="www.lab.not.exist" />
180 <repeat name="other" >
181 <param name="field" value="notes" />
182 <param name="comment" value="Created in Galaxy" />
183 </repeat>
184 <repeat name="other" >
185 <param name="field" value="general" />
186 <param name="comment" value="Some other comment" />
187 </repeat>
188 </section>
189 <output name="out_tab">
190 <assert_contents>
191 <has_text text="assayData: 3 features, 2 samples " />
192 </assert_contents>
193 </output>
194 </test>
195 </tests>
196 <help><![CDATA[
197 Construct an ExpressionSet object from a variety of input attributes, such as experimentData, phenotype data, and annotations.
198
199 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>`_
200 .
201 ]]></help>
202 <citations>
203 <citation type="bibtex">
204 @misc{falcon2007introduction,
205 title={An introduction to bioconductor’s expressionset class},
206 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
207 year={2007}
208 }
209 </citation>
210 </citations>
211 </tool>