view inspect_eset.xml @ 1:817eb707bbf4 draft default tip

"planemo upload for repository commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
author bgruening
date Fri, 26 Nov 2021 15:54:31 +0000
parents 2fed32b5aa02
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<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>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf'
        <configfile name="conf" >

null_str_vec = function(gstr){
   tokens = unlist(as.vector(strsplit(gstr, split=",")))
   if (length(tokens) == 0){
   if (length(tokens) == 1){

rds_eset = readRDS('$rds_eset')
inspector = null_str_vec('$inspector')

        <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: -->
            <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="protocolData">Protocol Data</option>
            <option value="experimentData" >Experiment Data</option>
            <option value="annotation" >Annotation</option>
            <option value="signature" >Signature (requires Annotation)</option>
            <option value="abstract" >Abstract</option>
        <data name="out_tab" format="tabular" label="${} on ${on_string}: Inspection Result (${inspector})" />
        <test expect_num_outputs="1" >
            <!-- Inspect 0 -->
            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
            <param name="inspector" value="print" />
            <output name="out_tab" >
                    <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
        <test expect_num_outputs="1" >
            <!-- Inspect 1 -->
            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
            <param name="inspector" value="pData" />
            <output name="out_tab" >
                    <has_n_columns n="5" />
                    <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
        <test expect_num_outputs="1" >
            <!-- Inspect 2 -->
            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
            <param name="inspector" value="dims" />
            <output name="out_tab" >
                    <has_text_matching expression="Samples\s+\d{1,4}"/>
Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations.

For more options and information, consult `the manual <>`_ and the `rdocumentation <>`_
        <citation type="bibtex">
            title={An introduction to bioconductor’s expressionset class},
            author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},