Mercurial > repos > galaxyp > metaquantome_viz
changeset 7:8bd7734309f6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
| author | galaxyp |
|---|---|
| date | Mon, 18 Mar 2024 12:34:39 +0000 |
| parents | eb811f3018ea |
| children | |
| files | macros.xml metaquantome_viz.xml |
| diffstat | 2 files changed, 297 insertions(+), 319 deletions(-) [+] |
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--- a/macros.xml Wed Jun 16 19:59:28 2021 +0000 +++ b/macros.xml Mon Mar 18 12:34:39 2024 +0000 @@ -1,32 +1,37 @@ <macros> <token name="@TOOL_VERSION@">2.0.2</token> <token name="@VERSION_SUFFIX@">0</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">metaQuantome</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement> + <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement> <yield/> </requirements> </xml> <xml name="db"> - <param argument="db_tar" type="data" label="Database Archive File"/> + <param argument="db_tar" type="data" label="Database Archive File"/> </xml> <xml name="ONTOLOGY_ARGS"> - <conditional name="ontology_args"> - <param name="ontology" type="select" label="Ontology"> - <option value="go">Gene Ontology (GO terms)</option> - <option value="ec">Enzyme Commission (EC) numbers</option> - <option value="cog">Clusters of Orthologous Groups (COG categories)</option> - </param> - <when value="go"> - <param argument="--slim_down" type="boolean" label="Use slim GO"/> - </when> - <when value="ec"> - <!-- do nothing --> - </when> - <when value="cog"> - <!-- do nothing --> - </when> - </conditional> + <conditional name="ontology_args"> + <param name="ontology" type="select" label="Ontology"> + <option value="go">Gene Ontology (GO terms)</option> + <option value="ec">Enzyme Commission (EC) numbers</option> + <option value="cog">Clusters of Orthologous Groups (COG categories)</option> + </param> + <when value="go"> + <param argument="--slim_down" type="boolean" label="Use slim GO"/> + </when> + <when value="ec"> + <!-- do nothing --> + </when> + <when value="cog"> + <!-- do nothing --> + </when> + </conditional> </xml> <token name="@COMMON_PARAMS@"><![CDATA[ --samps '$samps' @@ -40,12 +45,12 @@ ]]> </token> <xml name="SAMPS"> - <param name="samps" type="data" format="tabular" label="Samples file" - help="must be created by 'metaQuantome: create samples file'"/> + <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/> </xml> <xml name="citations"> <citations> - <yield /> + <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation> + <yield/> </citations> </xml> </macros>
--- a/metaquantome_viz.xml Wed Jun 16 19:59:28 2021 +0000 +++ b/metaquantome_viz.xml Mon Mar 18 12:34:39 2024 +0000 @@ -3,79 +3,72 @@ <macros> <import>macros.xml</import> <xml name="barcol"> - <param argument="--barcol" type="select" label="Color for the bar fill"> - <option value="1">Blue</option> - <option value="2">Orange</option> - <option value="3">Yellow</option> - <option value="4">Red</option> - <option value="5">Violet</option> - <option value="6">Black</option> - <help> + <param argument="--barcol" type="select" label="Color for the bar fill"> + <option value="1">Blue</option> + <option value="2">Orange</option> + <option value="3">Yellow</option> + <option value="4">Red</option> + <option value="5">Violet</option> + <option value="6">Black</option> + <help> These same colors are also used in the heatmap and PCA plot, so the colors can be tweaked to match. Note that these colors are coded as 1 through 6 in the command line tool. </help> - </param> + </param> </xml> <xml name="common_bar_params"> - <param argument="--meancol" type="text" label="Mean intensity column name" - help="Mean intensity column name for desired experimental condition"> - <validator type="empty_field"/> - </param> - <param argument="--nterms" type="integer" - value="5" min="1" optional="true" - label="Number of terms to display" - help="leave blank for all terms"/> + <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition"> + <validator type="empty_field"/> + </param> + <param argument="--nterms" type="integer" value="5" min="1" optional="true" label="Number of terms to display" help="leave blank for all terms"/> </xml> <xml name="common_volc_params"> - <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> - <validator type="empty_field"/> - </param> - <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> - <validator type="empty_field"/> - </param> - <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" - help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/> - <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" - label="Flip the fold change (i.e., multiply log fold change by -1)"/> + <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> + <validator type="empty_field"/> + </param> + <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> + <validator type="empty_field"/> + </param> + <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/> + <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" label="Flip the fold change (i.e., multiply log fold change by -1)"/> </xml> <xml name="common_heatmap_params"> - <conditional name="heatmap"> - <param argument="--filter_to_sig" type="boolean" checked="false" - label="Only plot significant term" help="Necessitates use of results from `test`"/> - <when value="true"> - <param argument="--alpha" type="float" - value="0.05" min="0.0" max="1.0" - label="The q-value significance level"/> - <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> - <validator type="empty_field"/> - </param> - </when> - <when value="false"> - <!-- do nothing --> - </when> - </conditional> - <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/> - <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/> + <conditional name="heatmap"> + <param argument="--filter_to_sig" type="select" label="Only plot significant term" help="Necessitates use of results from `test`"> + <option value="true">Only plot significant term</option> + <option value="false">Plot all terms</option> + </param> + <when value="true"> + <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="The q-value significance level"/> + <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> + <validator type="empty_field"/> + </param> + </when> + <when value="false"> + <!-- do nothing --> + </when> + </conditional> + <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/> + <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/> </xml> <xml name="pca_calcsep"> - <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" - label="Calculate separation between groups and include in title?"/> + <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" label="Calculate separation between groups and include in title?"/> </xml> <xml name="target_onto"> - <param argument="--target_onto" type="select" optional="false" - label="GO category to restrict to"> - <help> + <param argument="--target_onto" type="select" optional="false" label="GO category to restrict to"> + <help> Only the values from this category of GO terms will be displayed. </help> - <option value="bp">Biological Process</option> - <option value="mf">Molecular Function</option> - <option value="cc">Cellular Component</option> - </param> + <option value="bp">Biological Process</option> + <option value="mf">Molecular Function</option> + <option value="cc">Cellular Component</option> + </param> </xml> </macros> - <expand macro="requirements" /> + <expand macro="xrefs"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import re #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier) @@ -172,294 +165,274 @@ ]]></command> <inputs> - <param argument="--infile" type="data" - format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/> - <expand macro="SAMPS"/> - <conditional name="mode_args"> - <param argument="--mode" type="select" label="Mode"> - <option value="f">Functional analysis</option> - <option value="t">Taxonomic analysis</option> - <option value="ft">Functional-taxonomic interaction analysis</option> - </param> - <when value="f"> - <param name="ontology" type="select" label="Ontology"> - <option value="go">Gene Ontology (GO terms)</option> - <option value="ec">Enzyme Commission (EC) numbers</option> - <option value="cog">Clusters of Orthologous Groups (COG categories)</option> - </param> - <conditional name="plot"> - <param argument="--plottype" type="select" label="Plot type"> - <option value="bar">Bar Chart (bar)</option> - <option value="volcano">Volcano Plot (volcano)</option> - <option value="heatmap">Heatmap (heatmap)</option> - <option value="pca">Principal Components Analysis (pca)</option> - </param> - <when value="bar"> - <expand macro="common_bar_params"/> - <expand macro="target_onto"/> - <expand macro="barcol"/> - </when> - <when value="volcano"> - <expand macro="common_volc_params"/> - <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" - label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/> - </when> - <when value="heatmap"> - <expand macro="common_heatmap_params"/> - </when> - <when value="pca"> - <expand macro="pca_calcsep"/> - </when> - </conditional> - </when> - <when value="t"> - <conditional name="plot"> - <param argument="--plottype" type="select" label="Plot type"> - <option value="bar">Bar Chart (bar)</option> - <option value="volcano">Volcano Plot (volcano)</option> - <option value="heatmap">Heatmap (heatmap)</option> - <option value="pca">Principal Components Analysis (pca)</option> + <param argument="--infile" type="data" format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/> + <expand macro="SAMPS"/> + <conditional name="mode_args"> + <param argument="--mode" type="select" label="Mode"> + <option value="f">Functional analysis</option> + <option value="t">Taxonomic analysis</option> + <option value="ft">Functional-taxonomic interaction analysis</option> </param> - <when value="bar"> - <param argument="--target_rank" type="select" - label="Taxonomic rank to restrict to in the plot" - help="possibilities are taken from the input dataset."> - <options from_dataset="infile"> - <column name="value" index="2"/> - <filter type="unique_value" name="unique_taxon" column="2"/> - <!-- <filter type="remove_value" value="rank" column="2"/> --> - </options> - </param> - <expand macro="common_bar_params"/> - <expand macro="barcol"/> - </when> - <when value="volcano"> - <expand macro="common_volc_params"/> - </when> - <when value="heatmap"> - <expand macro="common_heatmap_params"/> - </when> - <when value="pca"> - <expand macro="pca_calcsep"/> + <when value="f"> + <param name="ontology" type="select" label="Ontology"> + <option value="go">Gene Ontology (GO terms)</option> + <option value="ec">Enzyme Commission (EC) numbers</option> + <option value="cog">Clusters of Orthologous Groups (COG categories)</option> + </param> + <conditional name="plot"> + <param argument="--plottype" type="select" label="Plot type"> + <option value="bar">Bar Chart (bar)</option> + <option value="volcano">Volcano Plot (volcano)</option> + <option value="heatmap">Heatmap (heatmap)</option> + <option value="pca">Principal Components Analysis (pca)</option> + </param> + <when value="bar"> + <expand macro="common_bar_params"/> + <expand macro="target_onto"/> + <expand macro="barcol"/> + </when> + <when value="volcano"> + <expand macro="common_volc_params"/> + <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/> + </when> + <when value="heatmap"> + <expand macro="common_heatmap_params"/> + </when> + <when value="pca"> + <expand macro="pca_calcsep"/> + </when> + </conditional> </when> - </conditional> - </when> - <when value="ft"> - <conditional name="plot"> - <param argument="--plottype" type="select" label="Plot type"> - <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option> - </param> - <when value="ft_dist"> - <param argument="--meancol" type="text" label="Mean intensity column name" - help="Mean intensity column name for desired experimental condition"> - <validator type="empty_field"/> - </param> - <conditional name="margin"> - <param argument="--whichway" type="select" label="which distribution"> - <option value="f_dist">functional distribution for a taxon (f_dist)</option> - <option value="t_dist">taxonomic distribution for a function (t_dist)</option> - </param> - <when value="f_dist"> - <conditional name="term"> - <param name="id_or_name" type="select" label=""> - <option value="id" selected="true">Taxon ID</option> - <option value="name">Taxon name</option> + <when value="t"> + <conditional name="plot"> + <param argument="--plottype" type="select" label="Plot type"> + <option value="bar">Bar Chart (bar)</option> + <option value="volcano">Volcano Plot (volcano)</option> + <option value="heatmap">Heatmap (heatmap)</option> + <option value="pca">Principal Components Analysis (pca)</option> </param> - <when value="id"> - <param argument="--id" type="select" label="Taxon id"> + <when value="bar"> + <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset."> <options from_dataset="infile"> - <column name="value" index="3"/> - <filter type="unique_value" column="3"/> - <!-- <filter type="remove_value" value="tax_id"/> --> + <column name="value" index="2"/> + <filter type="unique_value" name="unique_taxon" column="2"/> + <!-- <filter type="remove_value" value="rank" column="2"/> --> </options> </param> + <expand macro="common_bar_params"/> + <expand macro="barcol"/> </when> - <when value="name"> - <param argument="--name" type="select" label="Taxon name"> - <options from_dataset="infile"> - <column name="value" index="4"/> - <filter type="unique_value" column="4"/> - <!-- <filter type="remove_value" value="taxon_name"/> --> - </options> - </param> + <when value="volcano"> + <expand macro="common_volc_params"/> </when> - </conditional> - <expand macro="target_onto"/> - </when> - <when value="t_dist"> - <conditional name="term"> - <param name="id_or_name" type="select" label=""> - <option value="id" selected="true">Functional term ID</option> - <option value="name">Functional term name</option> - </param> - <when value="id"> - <param argument="--id" type="select" label="Functional term id"> - <options from_dataset="infile"> - <column name="value" index="0"/> - <filter type="unique_value" column="0"/> - <!-- <filter type="remove_value" value="go_id"/> --> - </options> - </param> + <when value="heatmap"> + <expand macro="common_heatmap_params"/> + </when> + <when value="pca"> + <expand macro="pca_calcsep"/> </when> - <when value="name"> - <param argument="--name" type="select" label="Functional term name"> - <options from_dataset="infile"> - <column name="value" index="1"/> - <filter type="unique_value" column="1"/> - <!-- <filter type="remove_value" value="name"/> --> - </options> - </param> + </conditional> + </when> + <when value="ft"> + <conditional name="plot"> + <param argument="--plottype" type="select" label="Plot type"> + <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option> + </param> + <when value="ft_dist"> + <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition"> + <validator type="empty_field"/> + </param> + <conditional name="margin"> + <param argument="--whichway" type="select" label="which distribution"> + <option value="f_dist">functional distribution for a taxon (f_dist)</option> + <option value="t_dist">taxonomic distribution for a function (t_dist)</option> + </param> + <when value="f_dist"> + <conditional name="term"> + <param name="id_or_name" type="select" label=""> + <option value="id" selected="true">Taxon ID</option> + <option value="name">Taxon name</option> + </param> + <when value="id"> + <param argument="--id" type="select" label="Taxon id"> + <options from_dataset="infile"> + <column name="value" index="3"/> + <filter type="unique_value" column="3"/> + <!-- <filter type="remove_value" value="tax_id"/> --> + </options> + </param> + </when> + <when value="name"> + <param argument="--name" type="select" label="Taxon name"> + <options from_dataset="infile"> + <column name="value" index="4"/> + <filter type="unique_value" column="4"/> + <!-- <filter type="remove_value" value="taxon_name"/> --> + </options> + </param> + </when> + </conditional> + <expand macro="target_onto"/> + </when> + <when value="t_dist"> + <conditional name="term"> + <param name="id_or_name" type="select" label=""> + <option value="id" selected="true">Functional term ID</option> + <option value="name">Functional term name</option> + </param> + <when value="id"> + <param argument="--id" type="select" label="Functional term id"> + <options from_dataset="infile"> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + <!-- <filter type="remove_value" value="go_id"/> --> + </options> + </param> + </when> + <when value="name"> + <param argument="--name" type="select" label="Functional term name"> + <options from_dataset="infile"> + <column name="value" index="1"/> + <filter type="unique_value" column="1"/> + <!-- <filter type="remove_value" value="name"/> --> + </options> + </param> + </when> + </conditional> + <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset."> + <options from_dataset="infile"> + <column name="value" index="5"/> + <filter type="unique_value" name="unique_taxon" column="5"/> + <!-- <filter type="remove_value" value="rank" column="5"/> --> + </options> + </param> + </when> + </conditional> + <expand macro="barcol"/> </when> - </conditional> - <param argument="--target_rank" type="select" - label="Taxonomic rank to restrict to in the plot" - help="possibilities are taken from the input dataset."> - <options from_dataset="infile"> - <column name="value" index="5"/> - <filter type="unique_value" name="unique_taxon" column="5"/> - <!-- <filter type="remove_value" value="rank" column="5"/> --> - </options> - </param> - </when> - </conditional> - <expand macro="barcol"/> + </conditional> </when> - </conditional> - </when> - </conditional> - <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> - <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/> + </conditional> + <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> + <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/> </inputs> <outputs> - <data format="html" name="wrapped_outfile" - label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" - from_work_dir="wrapped_outfile.html"/> - <data format="tabular" name="plotdata" - label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data" - from_work_dir="plotdata.tab"> - <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> - </data> - - <data format="tabular" name="heatmap_feature_cluster" - label="${mode_args.plot.plottype}: feature cluster data" - from_work_dir="feature_cluster_data.txt"> - <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> - </data> - <data format="tabular" name="heatmap_sample_cluster" - label="${mode_args.plot.plottype}: sample cluster data" - from_work_dir="sample_cluster_data.txt"> - <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> - </data> - - <data format="tabular" name="pca_sample_cluster" - label="${mode_args.plot.plottype}: sample cluster data" - from_work_dir="PC_Data.txt"> - <filter>mode_args['plot']['plottype'] in ["pca"]</filter> - </data> - + <data format="html" name="wrapped_outfile" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" from_work_dir="wrapped_outfile.html"/> + <data format="tabular" name="plotdata" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data" from_work_dir="plotdata.tab"> + <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> + </data> + <data format="tabular" name="heatmap_feature_cluster" label="${mode_args.plot.plottype}: feature cluster data" from_work_dir="feature_cluster_data.txt"> + <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> + </data> + <data format="tabular" name="heatmap_sample_cluster" label="${mode_args.plot.plottype}: Heatmap sample cluster data" from_work_dir="sample_cluster_data.txt"> + <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> + </data> + <data format="tabular" name="pca_sample_cluster" label="${mode_args.plot.plottype}: PCA sample cluster data" from_work_dir="PC_Data.txt"> + <filter>mode_args['plot']['plottype'] in ["pca"]</filter> + </data> </outputs> <tests> <test expect_num_outputs="2"> - <param name="infile" value="tax_filt_out.tab" ftype="tabular"/> - <param name="mode" value="t" /> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="bar" /> - <param name="target_rank" value="genus" /> - <param name="meancol" value="NS_mean" /> - <output name="wrapped_outfile"> + <param name="infile" value="tax_filt_out.tab" ftype="tabular"/> + <param name="mode" value="t"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="bar"/> + <param name="target_rank" value="genus"/> + <param name="meancol" value="NS_mean"/> + <output name="wrapped_outfile"> <assert_contents> - <has_text text="To download the image" /> + <has_text text="To download the image"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> - <param name="infile" value="tax_test_out.tab" ftype="tabular"/> - <param name="mode" value="t" /> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="volcano" /> - <param name="target_rank" value="genus" /> - <param name="fc_name" value="log2fc_NS_over_WS" /> - <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> - <param name="textannot" value="taxon_name" /> - <output name="wrapped_outfile"> + <param name="infile" value="tax_test_out.tab" ftype="tabular"/> + <param name="mode" value="t"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="volcano"/> + <param name="target_rank" value="genus"/> + <param name="fc_name" value="log2fc_NS_over_WS"/> + <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> + <param name="textannot" value="taxon_name"/> + <output name="wrapped_outfile"> <assert_contents> - <has_text text="To download the image" /> + <has_text text="To download the image"/> </assert_contents> </output> </test> <test expect_num_outputs="3"> <param name="infile" value="tax_test_out.tab" ftype="tabular"/> - <param name="mode" value="t" /> + <param name="mode" value="t"/> <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="heatmap" /> - <param name="filter_to_sig" /> - <param name="alpha" value="0.05" /> - <param name="fc_corr_p" value="corrected_p_NS_over_WS" /> - <param name="feature_cluster_size" value="2" /> - <param name="sample_cluster_size" value="2" /> + <param name="plottype" value="heatmap"/> + <param name="filter_to_sig"/> + <param name="alpha" value="0.05"/> + <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> + <param name="feature_cluster_size" value="2"/> + <param name="sample_cluster_size" value="2"/> <output name="wrapped_outfile"> - <assert_contents> - <has_text text="To download the image" /> - </assert_contents> + <assert_contents> + <has_text text="To download the image"/> + </assert_contents> </output> <output name="heatmap_feature_cluster"> - <assert_contents> - <has_text text="481" /> - </assert_contents> + <assert_contents> + <has_text text="481"/> + </assert_contents> </output> </test> <test expect_num_outputs="2"> - <param name="infile" value="tax_test_out.tab" ftype="tabular"/> - <param name="mode" value="t" /> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="pca" /> - <output name="wrapped_outfile"> + <param name="infile" value="tax_test_out.tab" ftype="tabular"/> + <param name="mode" value="t"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="pca"/> + <output name="wrapped_outfile"> <assert_contents> - <has_text text="To download the image" /> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> - <param name="mode" value="f" /> - <param name="ontology" value="go" /> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="bar" /> - <param name="meancol" value="NS_mean" /> - <param name="target_onto" value="bp"/> - <output name="wrapped_outfile"> - <assert_contents> - <has_text text="To download the image" /> + <has_text text="To download the image"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> - <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> - <param name="mode" value="f" /> - <param name="ontology" value="go"/> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="volcano" /> - <param name="fc_name" value="log2fc_NS_over_WS" /> - <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> - <output name="wrapped_outfile"> + <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> + <param name="mode" value="f"/> + <param name="ontology" value="go"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="bar"/> + <param name="meancol" value="NS_mean"/> + <param name="target_onto" value="bp"/> + <output name="wrapped_outfile"> <assert_contents> - <has_text text="To download the image" /> + <has_text text="To download the image"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> + <param name="mode" value="f"/> + <param name="ontology" value="go"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="volcano"/> + <param name="fc_name" value="log2fc_NS_over_WS"/> + <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> + <output name="wrapped_outfile"> + <assert_contents> + <has_text text="To download the image"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> - <param name="infile" value="tf_filt_out.tab" ftype="tabular"/> - <param name="mode" value="ft" /> - <param name="samps" value="rudney_samples.tab" ftype="tabular"/> - <param name="plottype" value="ft_dist" /> - <param name="meancol" value="NS_mean" /> - <param name="whichway" value="f_dist" /> - <param name="id_or_name" value="id" /> - <param name="id" value="1301" /> - <param name="target_onto" value="bp" /> - <output name="wrapped_outfile"> + <param name="infile" value="tf_filt_out.tab" ftype="tabular"/> + <param name="mode" value="ft"/> + <param name="samps" value="rudney_samples.tab" ftype="tabular"/> + <param name="plottype" value="ft_dist"/> + <param name="meancol" value="NS_mean"/> + <param name="whichway" value="f_dist"/> + <param name="id_or_name" value="id"/> + <param name="id" value="1301"/> + <param name="target_onto" value="bp"/> + <output name="wrapped_outfile"> <assert_contents> - <has_text text="To download the image" /> + <has_text text="To download the image"/> </assert_contents> </output> </test> @@ -483,5 +456,5 @@ Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>