Mercurial > repos > bgruening > music_construct_eset

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 7b4e1e85d9d288a904444eb9fcb96bcdc856b9ff
author bgruening
date Wed, 06 Nov 2024 23:21:28 +0000
parents 282819d09a4f
children
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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="21.09" 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="xrefs"/>
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8 <expand macro="requirements" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 cat '$conf' >> /dev/stderr &&
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11 Rscript --vanilla '$conf'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="conf" >
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16 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
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17 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
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18
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19 null_str_vec = function(gstr, is.str=FALSE){
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20 tokens = unlist(as.vector(strsplit(gstr, split=",")))
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21 if (length(tokens) == 0){
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22 if (is.str){
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23 return(character(0))
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24 }
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25 return(NULL)
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26 }
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27 if (length(tokens) == 1){
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28 return(tokens[[1]])
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29 }
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30 return(tokens)
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31 }
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32
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33 ## Assay Data
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34 ## F rows of features and S columns of samples
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35 ## - This file is the only non-optional parameter
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36 exprs_file = '$exprs_file'
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37 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
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38 row.names = 1, as.is = T, check.names=FALSE))
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39 ## Phenotype Data
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40 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
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41 pdata = NULL
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42 #if '$pdata_file':
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43 pdata_file = '$pdata_file'
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44 pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T, check.names=FALSE)
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45 #end if
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46 ## Annotation and Feature Data, or just a string for type of chip used
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47 annotation = null_str_vec('$annotation')
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48 if (is.null(annotation)){
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49 annotation = character(0)
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50 }
0
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51
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52 if (all(rownames(pdata) != colnames(exprs))) {
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53 stop("Number of Samples between phenotypes and assays are not the same")
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54 }
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55
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56 ##metadata = data.frame(
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57 ## labelDescription = c(
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58 ## "Patient gender",
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59 ## "Case/Control",
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60 ## "Tumor progress"),
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61 ## row.names = c("gender", "type", "score"))
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62 metadata = as.data.frame(do.call(rbind, list(
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63 #for i, row in enumerate($metadata):
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64 #if i==0
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65 list(ldesc='$row.label_desc', lname='$row.row_names')
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66 #else
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67 ,list(ldesc='$row.label_desc', lname='$row.row_names')
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68 #end if
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69 #end for
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70 )))
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71 metadata\$labelDescription = unlist(metadata\$ldesc)
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72 rownames(metadata) = unlist(metadata\$lname)
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73 metadata\$ldesc = NULL
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74 metadata\$lname = NULL
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75
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76 if (nrow(metadata)==0) {
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77 pheno_data = new("AnnotatedDataFrame", data = pdata)
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78 } else {
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79 pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
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80 }
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81
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82
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83 ## Experiment Description -- using the MIAME object
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84 experiment_data = new(
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85 "MIAME",
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86 name = null_str_vec('$expdata.name', is.str=T),
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87 lab = null_str_vec('$expdata.lab', is.str=T),
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88 contact = null_str_vec('$expdata.contact', is.str=T),
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89 title = null_str_vec('$expdata.title', is.str=T),
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90 abstract = null_str_vec('$expdata.abstract', is.str=T),
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91 url = null_str_vec('$expdata.url', is.str=T),
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92 other = list(
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93 #for i, row in enumerate($expdata.other):
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94 #if i==0
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95 '$row.field' = null_str_vec('$row.comment', is.str=T)
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96 #else
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97 ,'$row.field' = null_str_vec('$row.comment', is.str=T)
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98 #end if
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99 #end for
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100 ))
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101
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102 e_set = ExpressionSet(assayData = exprs,
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103 phenoData = pheno_data,
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104 experimentData = experiment_data,
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105 annotation = annotation)
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106
1
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107 capture.output(print(e_set), file = '$out_txt')
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108 print(e_set)
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109 saveRDS(e_set, file= '$out_rds')
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110
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111 </configfile>
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112 </configfiles>
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113 <inputs>
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114 <param name="exprs_file" label="Assay Data" type="data" format="tabular,tsv"
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115 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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116 <param name="pdata_file" label="Phenotype Data" type="data"
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117 format="tabular,tsv" optional="true"
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118 help="S rows of samples, and V columns of covariates (e.g. sex, age)" />
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119 <param name="annotation" label="Annotation" type="text"
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120 optional="true" help="A string detailing which chip was used" >
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121 <expand macro="validator_text_and_urls" />
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122 </param>
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123 <repeat name="metadata" title="Meta Data" min="0" max="15" >
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124 <!-- optional, so min=0 -->
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125 <param name="row_names" label="Label" type="text"
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126 help="Metadata should correspond directly to the columns of the Phenotype Data" >
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127 <expand macro="validator_text_and_urls" />
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128 </param>
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129 <param name="label_desc" label="Label Description" type="text" >
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130 <expand macro="validator_text_and_urls" />
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131 </param>
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132 </repeat>
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133 <section name="expdata" title="Experiment Data" >
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134 <param name="name" label="Experimenter Name" 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="lab" label="Lab" 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="contact" label="Contact" 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="title" label="Title" 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="abstract" label="Abstract" 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 <param name="url" label="URL" type="text" value="" optional="true" >
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150 <expand macro="validator_text_and_urls" />
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151 </param>
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152 <repeat name="other" title="Other Fields" min="1">
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153 <param name="field" label="FieldName" type="text" value="notes" >
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154 <expand macro="validator_text_and_urls" />
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155 </param>
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156 <param name="comment" label="Comment" type="text" value="Created in Galaxy" >
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157 <expand macro="validator_text_and_urls" />
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158 </param>
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159 </repeat>
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160 </section>
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161 </inputs>
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162 <outputs>
1
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163 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
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164 <data name="out_rds" format="@RDATATYPE@" label="${tool.name} on ${on_string}: RData ESet Object" />
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165 </outputs>
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166 <tests>
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167 <test expect_num_outputs="2" >
2
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168 <!-- Simple object -->
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169 <param name="exprs_file" value="mouse_scrna_exprs.tabular" />
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170 <param name="pdata_file" value="mouse_scrna_pheno.tabular" />
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171 <output name="out_txt">
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172 <assert_contents>
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173 <has_text text="assayData: 100 features, 100 samples " />
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174 </assert_contents>
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175 </output>
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176 </test>
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177 <test expect_num_outputs="2" >
0
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178 <!-- Values from the manual -->
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179 <param name="exprs_file" value="array.tsv" />
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180 <param name="pdata_file" value="pheno.tsv" />
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181 <param name="annotation" value="hgu95av2" />
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182 <repeat name="metadata" >
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183 <param name="row_names" value="gender" />
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184 <param name="label_desc" value="Patient gender" />
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185 </repeat>
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186 <repeat name="metadata" >
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187 <param name="row_names" value="type" />
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188 <param name="label_desc" value="Case/control status" />
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189 </repeat>
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190 <repeat name="metadata" >
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191 <param name="row_names" value="score" />
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192 <param name="label_desc" value="Tumor Progress on XYZ scale" />
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193 </repeat>
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194 <section name="expdata">
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195 <param name="name" value="Pierre Fermat" />
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196 <param name="lab" value="Francis Galton Lab" />
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197 <param name="contact" value="pfermat@lab.not.exist" />
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198 <param name="title" value="Smoking-Cancer Experiment" />
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199 <param name="abstract" value="An example ExpressionSet" />
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200 <param name="url" value="www.lab.not.exist" />
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201 <repeat name="other" >
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202 <param name="field" value="notes" />
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203 <param name="comment" value="Created in Galaxy" />
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204 </repeat>
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205 <repeat name="other" >
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206 <param name="field" value="general" />
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207 <param name="comment" value="Some other comment" />
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208 </repeat>
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209 </section>
1
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210 <output name="out_txt">
0
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211 <assert_contents>
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212 <has_text text="assayData: 3 features, 2 samples " />
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213 </assert_contents>
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214 </output>
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215 </test>
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216 </tests>
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217 <help><![CDATA[
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218 Construct an ExpressionSet object from a variety of input attributes, such as experimentData, phenotype data, and annotations.
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219
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220 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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221 .
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222 ]]></help>
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223 <citations>
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224 <citation type="bibtex">
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225 @misc{falcon2007introduction,
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226 title={An introduction to bioconductor’s expressionset class},
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227 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
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228 year={2007}
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229 }
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230 </citation>
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231 </citations>
8
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232 </tool>