diff metaquantome_viz.xml @ 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 9bf325045235
children
line wrap: on
line diff
--- 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>