Mercurial > repos > bgruening > music_inspect_eset

annotate inspect_eset.xml @ 3:8c64a2da3869 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
author bgruening
date Thu, 10 Feb 2022 12:52:56 +0000
parents 577435e5e6b2
children 7705cc75ac18
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1 <tool id="music_inspect_eset" name="Inspect 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>Inspect an ExpressionSet object by a variety of attributes</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 '$conf'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="conf" >
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14 null_str_vec = function(gstr){
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15 tokens = unlist(as.vector(strsplit(gstr, split=",")))
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16 if (length(tokens) == 0){
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17 return(NULL)
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18 }
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19 if (length(tokens) == 1){
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20 return(tokens[[1]])
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21 }
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22 return(tokens)
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23 }
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25 rds_eset = readRDS('$rds_eset')
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26 inspector = null_str_vec('$inspector')
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27 outfile_tab='$out_tab'
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28
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29 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
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30 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
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32 printout = function(text) {
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33 if (typeof(text) %in% c("list", "vector", "integer", "double", "numeric")) {
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34 write.table(text, file = outfile_tab, quote = F, sep = "\t",
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35 col.names = NA)
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36 } else {
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37 ## text
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38 print(typeof(text))
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39 capture.output(text, file = outfile_tab) # nolint
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40 }
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41 }
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42
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43 if (inspector %in% c("print", "pData", "fData", "dims",
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44 "experimentData", "protocolData", "exprs",
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45 "signature", "annotation", "abstract")) {
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46 op = get(inspector)
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47 tab = op(rds_eset)
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48 printout(tab)
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49 } else {
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50 stop(paste0("No such option:", inspector))
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51 }
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52
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53
0
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54 </configfile>
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55 </configfiles>
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56 <inputs>
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57 <param name="rds_eset" label="ESet Dataset" type="data" format="@RDATATYPE@" />
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58 <param name="inspector" label="Inspect" type="select"
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59 help="Inspect an aspect of the ESet dataset" >
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60 <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
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61 <option value="print" selected="true">General Information</option>
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62 <option value="exprs" >Expression Data Table</option>
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63 <option value="pData" >PhenoType Data Table</option>
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64 <option value="fData" >Feature Data Table</option>
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65 <option value="dims" >Dimension</option>
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66 <option value="protocolData">Protocol Data</option>
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67 <option value="experimentData" >Experiment Data</option>
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68 <option value="annotation" >Annotation</option>
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69 <option value="signature" >Signature (requires Annotation)</option>
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70 <option value="abstract" >Abstract</option>
0
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71 </param>
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72 </inputs>
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73 <outputs>
1
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74 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result (${inspector})" />
0
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75 </outputs>
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76 <tests>
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77 <test expect_num_outputs="1" >
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78 <!-- Inspect 0 -->
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79 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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80 <param name="inspector" value="print" />
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81 <output name="out_tab" >
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82 <assert_contents>
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83 <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test expect_num_outputs="1" >
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88 <!-- Inspect 1 -->
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89 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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90 <param name="inspector" value="pData" />
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91 <output name="out_tab" >
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92 <assert_contents>
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93 <has_n_columns n="5" />
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94 <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test expect_num_outputs="1" >
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99 <!-- Inspect 2 -->
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100 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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101 <param name="inspector" value="dims" />
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102 <output name="out_tab" >
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103 <assert_contents>
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104 <has_text_matching expression="Samples\s+\d{1,4}"/>
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105 </assert_contents>
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106 </output>
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations.
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111
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112 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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113 .
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114 ]]></help>
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115 <citations>
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116 <citation type="bibtex">
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117 @misc{falcon2007introduction,
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118 title={An introduction to bioconductor’s expressionset class},
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119 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
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120 year={2007}
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121 }
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122 </citation>
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123 </citations>
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124 </tool>