Mercurial > repos > bgruening > music_inspect_eset
diff inspect_eset.xml @ 0:2fed32b5aa02 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
author | bgruening |
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date | Sun, 12 Sep 2021 19:48:26 +0000 |
parents | |
children | 817eb707bbf4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/inspect_eset.xml Sun Sep 12 19:48:26 2021 +0000 @@ -0,0 +1,99 @@ +<tool id="music_inspect_eset" name="Inspect Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + profile="20.05" license="GPL-3.0-or-later" > + <description>Inspect an ExpressionSet object by a variety of attributes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf' +]]></command> + <configfiles> + <configfile name="conf" > + +null_str_vec = function(gstr){ + tokens = unlist(as.vector(strsplit(gstr, split=","))) + if (length(tokens) == 0){ + return(NULL) + } + if (length(tokens) == 1){ + return(tokens[[1]]) + } + return(tokens) +} + +rds_eset = readRDS('$rds_eset') +inspector = null_str_vec('$inspector') +outfile_tab='$out_tab' + + </configfile> + </configfiles> + <inputs> + <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" /> + <param name="inspector" label="Inspect" type="select" + help="Inspect an aspect of the ESet dataset" > + <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet --> + <option value="print" selected="true">General Information</option> + <option value="exprs" >Expression Data Table</option> + <option value="pData" >PhenoType Data Table</option> + <option value="fData" >Feature Data Table</option> + <option value="dims" >Dimension</option> + <option value="experimentData" /> + <option value="signature" /> + <option value="annotation" /> + <option value="abstract" /> + </param> + </inputs> + <outputs> + <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result" /> + </outputs> + <tests> + <test expect_num_outputs="1" > + <!-- Inspect 0 --> + <param name="rds_eset" value="EMTABesethealthy.subset.rds" /> + <param name="inspector" value="print" /> + <output name="out_tab" > + <assert_contents> + <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Inspect 1 --> + <param name="rds_eset" value="EMTABesethealthy.subset.rds" /> + <param name="inspector" value="pData" /> + <output name="out_tab" > + <assert_contents> + <has_n_columns n="5" /> + <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Inspect 2 --> + <param name="rds_eset" value="EMTABesethealthy.subset.rds" /> + <param name="inspector" value="dims" /> + <output name="out_tab" > + <assert_contents> + <has_n_columns n="1" /> + <has_text_matching expression="Samples\s+\d{1,4}"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations. + +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>`_ +. + ]]></help> + <citations> + <citation type="bibtex"> + @misc{falcon2007introduction, + title={An introduction to bioconductor’s expressionset class}, + author={Falcon, Seth and Morgan, Martin and Gentleman, Robert}, + year={2007} + } + </citation> + </citations> +</tool> \ No newline at end of file