annotate construct_eset.xml @ 2:7902cd31b9b5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
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date Sat, 29 Jan 2022 12:52:10 +0000
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1 <tool id="music_construct_eset" name="Construct Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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2 profile="20.05" license="GPL-3.0-or-later" >
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3 <description>Create an ExpressionSet object from tabular and textual data</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript --vanilla '$conf'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="conf" >
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13
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14 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
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15 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
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16
1
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17 null_str_vec = function(gstr, is.str=FALSE){
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18 tokens = unlist(as.vector(strsplit(gstr, split=",")))
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19 if (length(tokens) == 0){
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20 if (is.str){
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21 return(character(0))
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22 }
0
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23 return(NULL)
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24 }
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25 if (length(tokens) == 1){
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26 return(tokens[[1]])
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27 }
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28 return(tokens)
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29 }
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30
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31 ## Assay Data
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32 ## F rows of features and S columns of samples
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33 ## - This file is the only non-optional parameter
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34 exprs_file = '$exprs_file'
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35 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
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36 row.names = 1, as.is = T, check.names=FALSE))
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37 ## Phenotype Data
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38 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
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39 pdata = NULL
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40 #if '$pdata_file':
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41 pdata_file = '$pdata_file'
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42 pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T, check.names=FALSE)
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43 #end if
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44 ## Annotation and Feature Data, or just a string for type of chip used
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45 annotation = null_str_vec('$annotation')
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46 if (is.null(annotation)){
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47 annotation = character(0)
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48 }
0
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49
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50 if (all(rownames(pdata) != colnames(exprs))) {
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51 stop("Number of Samples between phenotypes and assays are not the same")
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52 }
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53
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54 ##metadata = data.frame(
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55 ## labelDescription = c(
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56 ## "Patient gender",
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57 ## "Case/Control",
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58 ## "Tumor progress"),
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59 ## row.names = c("gender", "type", "score"))
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60 metadata = as.data.frame(do.call(rbind, list(
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61 #for i, row in enumerate($metadata):
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62 #if i==0
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63 list(ldesc='$row.label_desc', lname='$row.row_names')
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64 #else
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65 ,list(ldesc='$row.label_desc', lname='$row.row_names')
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66 #end if
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67 #end for
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68 )))
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69 metadata\$labelDescription = unlist(metadata\$ldesc)
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70 rownames(metadata) = unlist(metadata\$lname)
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71 metadata\$ldesc = NULL
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72 metadata\$lname = NULL
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73
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74 if (nrow(metadata)==0) {
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75 pheno_data = new("AnnotatedDataFrame", data = pdata)
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76 } else {
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77 pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
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78 }
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79
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80
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81 ## Experiment Description -- using the MIAME object
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82 experiment_data = new(
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83 "MIAME",
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84 name = null_str_vec('$expdata.name', is.str=T),
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85 lab = null_str_vec('$expdata.lab', is.str=T),
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86 contact = null_str_vec('$expdata.contact', is.str=T),
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87 title = null_str_vec('$expdata.title', is.str=T),
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88 abstract = null_str_vec('$expdata.abstract', is.str=T),
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89 url = null_str_vec('$expdata.url', is.str=T),
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90 other = list(
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91 #for i, row in enumerate($expdata.other):
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92 #if i==0
1
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93 '$row.field' = null_str_vec('$row.comment', is.str=T)
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94 #else
1
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95 ,'$row.field' = null_str_vec('$row.comment', is.str=T)
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96 #end if
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97 #end for
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98 ))
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99
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100 e_set = ExpressionSet(assayData = exprs,
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101 phenoData = pheno_data,
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102 experimentData = experiment_data,
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103 annotation = annotation)
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104
1
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105 capture.output(print(e_set), file = '$out_txt')
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106 saveRDS(e_set, file= '$out_rds')
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107
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108 </configfile>
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109 </configfiles>
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110 <inputs>
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111 <param name="exprs_file" label="Assay Data" type="data" format="tabular,tsv"
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112 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." />
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113 <param name="pdata_file" label="Phenotype Data" type="data"
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114 format="tabular,tsv" optional="true"
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115 help="S rows of samples, and V columns of covariates (e.g. sex, age)" />
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116 <param name="annotation" label="Annotation" type="text"
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117 optional="true" help="A string detailing which chip was used" >
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118 <expand macro="validator_text_and_urls" />
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119 </param>
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120 <repeat name="metadata" title="Meta Data" min="0" max="15" >
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121 <!-- optional, so min=0 -->
1
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122 <param name="row_names" label="Label" type="text"
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123 help="Metadata should correspond directly to the columns of the Phenotype Data" >
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124 <expand macro="validator_text_and_urls" />
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125 </param>
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126 <param name="label_desc" label="Label Description" type="text" >
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127 <expand macro="validator_text_and_urls" />
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128 </param>
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129 </repeat>
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130 <section name="expdata" title="Experiment Data" >
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131 <param name="name" label="Experimenter Name" type="text" value="" optional="true" >
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132 <expand macro="validator_text_and_urls" />
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133 </param>
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134 <param name="lab" label="Lab" type="text" value="" optional="true" >
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135 <expand macro="validator_text_and_urls" />
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136 </param>
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137 <param name="contact" label="Contact" type="text" value="" optional="true" >
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138 <expand macro="validator_text_and_urls" />
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139 </param>
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140 <param name="title" label="Title" type="text" value="" optional="true" >
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141 <expand macro="validator_text_and_urls" />
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142 </param>
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143 <param name="abstract" label="Abstract" type="text" value="" optional="true" >
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144 <expand macro="validator_text_and_urls" />
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145 </param>
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146 <param name="url" label="URL" type="text" value="" optional="true" >
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147 <expand macro="validator_text_and_urls" />
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148 </param>
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149 <repeat name="other" title="Other Fields" min="1">
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150 <param name="field" label="FieldName" type="text" value="notes" >
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151 <expand macro="validator_text_and_urls" />
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152 </param>
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153 <param name="comment" label="Comment" type="text" value="Created in Galaxy" >
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154 <expand macro="validator_text_and_urls" />
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155 </param>
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156 </repeat>
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157 </section>
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158 </inputs>
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159 <outputs>
1
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160 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
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161 <data name="out_rds" format="@RDATATYPE@" label="${tool.name} on ${on_string}: RData ESet Object" />
0
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162 </outputs>
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163 <tests>
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164 <test expect_num_outputs="2" >
2
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165 <!-- Simple object -->
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166 <param name="exprs_file" value="mouse_scrna_exprs.tabular" />
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167 <param name="pdata_file" value="mouse_scrna_pheno.tabular" />
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168 <output name="out_txt">
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169 <assert_contents>
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170 <has_text text="assayData: 100 features, 100 samples " />
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171 </assert_contents>
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172 </output>
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173 </test>
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174 <test expect_num_outputs="2" >
0
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175 <!-- Values from the manual -->
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176 <param name="exprs_file" value="array.tsv" />
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177 <param name="pdata_file" value="pheno.tsv" />
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178 <param name="annotation" value="hgu95av2" />
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179 <repeat name="metadata" >
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180 <param name="row_names" value="gender" />
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181 <param name="label_desc" value="Patient gender" />
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182 </repeat>
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183 <repeat name="metadata" >
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184 <param name="row_names" value="type" />
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185 <param name="label_desc" value="Case/control status" />
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186 </repeat>
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187 <repeat name="metadata" >
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188 <param name="row_names" value="score" />
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189 <param name="label_desc" value="Tumor Progress on XYZ scale" />
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190 </repeat>
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191 <section name="expdata">
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192 <param name="name" value="Pierre Fermat" />
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193 <param name="lab" value="Francis Galton Lab" />
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194 <param name="contact" value="pfermat@lab.not.exist" />
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195 <param name="title" value="Smoking-Cancer Experiment" />
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196 <param name="abstract" value="An example ExpressionSet" />
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197 <param name="url" value="www.lab.not.exist" />
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198 <repeat name="other" >
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199 <param name="field" value="notes" />
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200 <param name="comment" value="Created in Galaxy" />
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201 </repeat>
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202 <repeat name="other" >
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203 <param name="field" value="general" />
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204 <param name="comment" value="Some other comment" />
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205 </repeat>
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206 </section>
1
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207 <output name="out_txt">
0
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208 <assert_contents>
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209 <has_text text="assayData: 3 features, 2 samples " />
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210 </assert_contents>
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211 </output>
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212 </test>
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213 </tests>
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214 <help><![CDATA[
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215 Construct an ExpressionSet object from a variety of input attributes, such as experimentData, phenotype data, and annotations.
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216
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217 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>`_
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218 .
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219 ]]></help>
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220 <citations>
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221 <citation type="bibtex">
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222 @misc{falcon2007introduction,
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223 title={An introduction to bioconductor’s expressionset class},
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224 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
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225 year={2007}
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226 }
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227 </citation>
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228 </citations>
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229 </tool>