Mercurial > repos > bgruening > music_inspect_eset

annotate inspect_eset.xml @ 0:61596c07b5cc 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 19:46:18 +0000
parents
children 0638017a0189
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61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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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>
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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4 <macros>
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5 <import>macros.xml</import>
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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6 </macros>
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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7 <expand macro="requirements"/>
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf'
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10 ]]></command>
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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11 <configfiles>
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12 <configfile name="conf" >
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13
61596c07b5cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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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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24
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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='$out_tab'
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28
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29 </configfile>
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30 </configfiles>
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31 <inputs>
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32 <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" />
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33 <param name="inspector" label="Inspect" type="select"
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34 help="Inspect an aspect of the ESet dataset" >
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35 <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
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36 <option value="print" selected="true">General Information</option>
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37 <option value="exprs" >Expression Data Table</option>
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38 <option value="pData" >PhenoType Data Table</option>
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39 <option value="fData" >Feature Data Table</option>
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40 <option value="dims" >Dimension</option>
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41 <option value="experimentData" />
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42 <option value="signature" />
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43 <option value="annotation" />
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44 <option value="abstract" />
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result" />
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="1" >
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52 <!-- Inspect 0 -->
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53 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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54 <param name="inspector" value="print" />
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55 <output name="out_tab" >
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56 <assert_contents>
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57 <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 <test expect_num_outputs="1" >
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62 <!-- Inspect 1 -->
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63 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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64 <param name="inspector" value="pData" />
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65 <output name="out_tab" >
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66 <assert_contents>
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67 <has_n_columns n="5" />
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68 <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test expect_num_outputs="1" >
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73 <!-- Inspect 2 -->
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74 <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
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75 <param name="inspector" value="dims" />
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76 <output name="out_tab" >
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77 <assert_contents>
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78 <has_n_columns n="1" />
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79 <has_text_matching expression="Samples\s+\d{1,4}"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations.
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86
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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>`_
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88 .
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89 ]]></help>
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90 <citations>
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91 <citation type="bibtex">
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92 @misc{falcon2007introduction,
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93 title={An introduction to bioconductor’s expressionset class},
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94 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
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95 year={2007}
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96 }
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97 </citation>
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98 </citations>
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99 </tool>