cleaning macro

Author: nilchia

tools/flexynesis/flexynesis.xml

@@ -215,7 +215,7 @@
         #end if
     ]]></command>
     <inputs>
-        <expand macro="commercial_use"/>
+        <expand macro="commercial_use_param"/>
         <conditional name="training_type">
             <param name="model" type="select" label="Type of Analysis" >
                 <option value="s_train">Supervised training</option>
@@ -262,13 +262,13 @@
                     <when value="XGBoost"/>
                 </conditional>
                 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
-                    <expand macro="sanitizer"/>
+                    <expand macro="sanitizer_printable"/>
                 </param>
                 <param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">
-                    <expand macro="sanitizer"/>
+                    <expand macro="sanitizer_printable"/>
                 </param>
                 <param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">
-                    <expand macro="sanitizer"/>
+                    <expand macro="sanitizer_printable"/>
                 </param>
                 <expand macro="advanced"/>
             </when>
@@ -314,7 +314,7 @@
                         <option value="pca" selected="true">PCA</option>
                         <option value="umap">UMAP</option>
                     </param>
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_km_conditional">
@@ -326,9 +326,9 @@
                 </when>
                 <when value="yes">
                     <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred.">
-                        <expand macro="sanitizer"/>
+                        <expand macro="sanitizer_printable"/>
                     </param>
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_cox_conditional">
@@ -340,18 +340,18 @@
                 </when>
                 <when value="yes">
                     <param name="omics_name" type="text" label="Omics layer to use for cox input" optional="false" help="If not specified, the first omics layer will be used.">
-                        <expand macro="sanitizer"/>
+                        <expand macro="sanitizer_printable"/>
                     </param>
                     <param name="clinical_variables" type="text" label="Clinical covariates" optional="true" help="Comma-separated list of clinical covariates to include in the Cox model (e.g SEX, AGE, ...).">
-                        <expand macro="sanitizer">
+                        <expand macro="sanitizer_printable">
                             <remove value=" "/>
                         </expand>
                     </param>
                     <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/>
                     <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred.">
-                        <expand macro="sanitizer"/>
+                        <expand macro="sanitizer_printable"/>
                     </param>
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_scatter_conditional">
@@ -362,7 +362,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_concordance_conditional">
@@ -373,7 +373,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_pr_curves_conditional">
@@ -384,7 +384,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_roc_curves_conditional">
@@ -395,7 +395,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
             <conditional name="plot_boxplot_conditional">
@@ -406,7 +406,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <expand macro="plots"/>
+                    <expand macro="plots_common_param"/>
                 </when>
             </conditional>
         </section>

tools/flexynesis/flexynesis_cbioportal_import.xml

@@ -30,7 +30,7 @@ with open(output_path, 'w') as f:
         ]]></configfile>
     </configfiles>
     <inputs>
-        <expand macro="commercial_use"/>
+        <expand macro="commercial_use_param"/>
         <param name="study_id" label="cBioPortal study ID" type="select" help="contact the administrator of this Galaxy instance if you miss a study ID">
             <options from_data_table="cbio"/>
         </param>

tools/flexynesis/flexynesis_plot.xml

@@ -47,7 +47,7 @@ from flexynesis_plot import (
     match_samples_to_embeddings
 )
 #if $plot_conditional.plot_type == "dimred":
-@PLOT_CONFIG@
+@PLOT_COMMON_CONFIG@
 embeddings, sample_names = load_embeddings('inputs/$plot_conditional.embeddings.element_identifier.$plot_conditional.embeddings.ext')
 matched_labels = match_samples_to_embeddings(sample_names, label_data)
 
@@ -63,7 +63,7 @@ fig = plot_dim_reduced(
 output_path = "plots/{label}_${plot_conditional.method}.${plot_conditional.format}"
 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
 #else if $plot_conditional.plot_type == "scatter":
-@PLOT_CONFIG@
+@PLOT_COMMON_CONFIG@
 
 true_label = label_data.columns[$plot_conditional.true_label-1]
 predicted_label = label_data.columns[$plot_conditional.predicted_label-1]
@@ -79,7 +79,7 @@ output_path = "plots/${plot_conditional.true_label}_${plot_conditional.predicted
 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
 
 #else if $plot_conditional.plot_type == "concordance_heatmap":
-@PLOT_CONFIG@
+@PLOT_COMMON_CONFIG@
 
 true_label = label_data.columns[$plot_conditional.true_label-1]
 predicted_label = label_data.columns[$plot_conditional.predicted_label-1]
@@ -92,21 +92,21 @@ output_path = "plots/{true_label}_{predicted_label}_concordance_heatmap.${plot_c
 fig.savefig(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
 
 #else if $plot_conditional.plot_type == "pr_curve":
-@PR_ROC_COMMON@
+@PR_ROC_CONFIG@
 
 fig = plot_pr_curves(y_true_np, y_probs_np)
 
 output_path = "plots/pr_curves.${plot_conditional.format}"
 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
 
 #else if $plot_conditional.plot_type == "roc_curve":
-@PR_ROC_COMMON@
+@PR_ROC_CONFIG@
 fig = plot_roc_curves(y_true_np, y_probs_np)
 output_path = "plots/roc_curves.${plot_conditional.format}"
 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
 
 #else if $plot_conditional.plot_type == "box_plot":
-@PR_ROC_BOX_COMMON@
+@PR_ROC_BOX_CONFIG@
 # Remove rows with missing data
 clean_data = label_data.dropna(subset=['known_label', 'probability'])
 
@@ -140,7 +140,7 @@ for class_label in classes:
         ]]></configfile>
     </configfiles>
     <inputs>
-        <expand macro="commercial_use"/>
+        <expand macro="commercial_use_param"/>
         <conditional name="plot_conditional">
             <param name="plot_type" type="select" label="Flexynesis plot">
                 <option value="dimred">Dimensionality reduction</option>
@@ -151,8 +151,8 @@ for class_label in classes:
                 <option value="box_plot">Box plot</option>
             </param>
             <when value="dimred">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                     <param argument="--embeddings" type="data" format="tabular,csv" label="Embeddings" help="Generated by flexynesis"/>
                     <param argument="--label" type="data_column" data_ref="labels" label="Column in the labels file to use for coloring the points in the plot"/>
                     <param name="method" type="select" label="Transformation method">
@@ -162,32 +162,32 @@ for class_label in classes:
                 </expand>
             </when>
             <when value="scatter">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                     <param name="true_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the true labels"/>
                     <param name="predicted_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the predicted labels"/>
                 </expand>
             </when>
             <when value="concordance_heatmap">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                     <param name="true_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the true labels"/>
                     <param name="predicted_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the predicted labels"/>
                 </expand>
             </when>
             <when value="pr_curve">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                 </expand>
             </when>
             <when value="roc_curve">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                 </expand>
             </when>
             <when value="box_plot">
-                <expand macro="plots">
-                    <expand macro="common_plot_input"/>
+                <expand macro="plots_common_param">
+                    <expand macro="plots_common_input"/>
                 </expand>
             </when>
         </conditional>

tools/flexynesis/flexynesis_utils.xml

@@ -136,7 +136,7 @@ with open(output_path, 'w') as f:
         ]]></configfile>
     </configfiles>
     <inputs>
-        <expand macro="commercial_use"/>
+        <expand macro="commercial_use_param"/>
         <conditional name="utils_conditional">
             <param name="util" type="select" label="Flexynesis utils">
                 <option value="louvain_clustering">Louvain Clustering</option>
@@ -148,23 +148,23 @@ with open(output_path, 'w') as f:
             </param>
             <when value="louvain_clustering">
                 <param argument="--X" type="data" format="tabular,csv" label="Matrix" help="Input matrix, (samples, features)"/>
-                <expand macro="common_plot_input"/>
+                <expand macro="plots_common_input"/>
                 <param argument="--threshold" type="float" min="0" optional="true" label="Distance threshold to create an edge between two nodes"/>
                 <param argument="--k" type="integer" min="0" optional="true" label="Number of nearest neighbors to connect for each node"/>
             </when>
             <when value="get_optimal_clusters">
                 <param argument="--X" type="data" format="tabular,csv" label="Matrix" help="Input matrix, (samples, features)"/>
-                <expand macro="common_plot_input"/>
+                <expand macro="plots_common_input"/>
                 <param argument="--min_k" type="integer" min="0" value="2" optional="false" label="Minimum number of clusters to try"/>
                 <param argument="--max_k" type="integer" min="0" value="10" optional="false" label="Maximum number of clusters to try"/>
             </when>
             <when value="k_means_clustering">
                 <param argument="--X" type="data" format="tabular,csv" label="Matrix" help="Input matrix, (samples, features)"/>
-                <expand macro="common_plot_input"/>
+                <expand macro="plots_common_input"/>
                 <param argument="--k" type="integer" min="0" optional="true" label="The number of clusters to form"/>
             </when>
             <when value="compute_ami_ari">
-                <expand macro="common_plot_input"/>
+                <expand macro="plots_common_input"/>
                     <param name="true_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the true labels"/>
                     <param name="predicted_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the predicted labels"/>
             </when>