Fix cummeRbund and various linting errors

tools/condense_characters/.lint_skip

@@ -0,0 +1,2 @@
+CitationsMissing
+ToolIDWhitespace

tools/condense_characters/.shed.yml

@@ -1,9 +1,10 @@
 categories:
 - Text Manipulation
 description: Condense consecutive characters.
+homepage_url: https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters
 long_description: |
   This tool condenses consecutive characters of the selected type.
 name: condense_characters
 owner: devteam
-remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters
+remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters
 type: unrestricted

tools/condense_characters/condense_characters.xml

@@ -1,10 +1,16 @@
-<tool id="Condense characters1" name="Condense"  version="1.0.0">
+<tool id="Condense characters1" name="Condense"  version="1.0.1" profile="24.0">
     <description>consecutive characters</description>
+    <requirements>
+        <requirement type="package" version="5.32">perl</requirement>
+    </requirements>
+    <required_files>
+        <include path="condense_characters.pl" />
+    </required_files>
     <command>
-        perl $__tool_directory__/condense_characters.pl
-            "${input}"
-            "${character}"
-            "${out_file1}"
+perl '$__tool_directory__/condense_characters.pl'
+'${input}'
+${character}
+'${out_file1}'
     </command>
     <inputs>
     <!--    <display>condense all consecutive $character from $input</display> -->
@@ -20,7 +26,7 @@
         <param format="txt" name="input" type="data" label="in this Query"/>
     </inputs>
     <outputs>
-        <data format="input" name="out_file1" metadata_source="input" />
+        <data format_source="input" name="out_file1" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -30,7 +36,6 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This tool condenses all consecutive characters of a specified type.

tools/cummerbund/.lint_skip

@@ -0,0 +1 @@
+InputsSelectDynamicOptions

tools/cummerbund/cummeRbund.R

@@ -1,14 +1,15 @@
 ## Feature Selection ##
 options(echo = TRUE)
 get_features <- function(my_genes, f = "gene") {
-    if (f == "isoforms")
+    if (f == "isoforms") {
         return(isoforms(my_genes))
-    else if (f == "tss")
+    } else if (f == "tss") {
         return(TSS(my_genes))
-    else if (f == "cds")
+    } else if (f == "cds") {
         return(CDS(my_genes))
-    else
+    } else {
         return(my_genes)
+    }
 }
 
 ## Main Function ##
@@ -62,67 +63,70 @@ cat(annotation(genes(cuff))[[1]], sep = ",")
 sink()
 
 png(filename = args$filename, width = args$width, height = args$height)
-tryCatch({
-    if (args$plotType == "density") {
-        csDensity(genes(cuff), replicates = args$replicates, logMode = args$log10)
-    } else if (args$plotType == "boxplot") {
-        csBoxplot(genes(cuff), replicates = args$replicates, logMode = args$log10)
-    } else if (args$plotType == "mds") {
-        MDSplot(genes(cuff), replicates = args$replicates)
-    } else if (args$plotType == "pca") {
-        PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
-    } else if (args$plotType == "dendrogram") {
-        csDendro(genes(cuff), replicates = args$replicates)
-    } else if (args$plotType == "scatter") {
-        if (args$gene_selector) {
-            my_genes <- get_features(getGenes(cuff, args$genes), args$features)
-        } else {
-            my_genes <- genes(cuff)
-        }
-        csScatter(my_genes, args$x, args$y, smooth = args$smooth, logMode = args$log10)
-    } else if (args$plotType == "volcano") {
-        if (args$gene_selector) {
-            my_genes <- get_features(getGenes(cuff, args$genes), args$features)
-        } else {
-            my_genes <- genes(cuff)
-        }
-        csVolcano(my_genes, args$x, args$y)
-    } else if (args$plotType == "heatmap") {
-        if (args$gene_selector) {
+tryCatch(
+    {
+        if (args$plotType == "density") {
+            csDensity(genes(cuff), replicates = args$replicates, logMode = args$log10)
+        } else if (args$plotType == "boxplot") {
+            csBoxplot(genes(cuff), replicates = args$replicates, logMode = args$log10)
+        } else if (args$plotType == "mds") {
+            MDSplot(genes(cuff), replicates = args$replicates)
+        } else if (args$plotType == "pca") {
+            PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
+        } else if (args$plotType == "dendrogram") {
+            csDendro(genes(cuff), replicates = args$replicates)
+        } else if (args$plotType == "scatter") {
+            if (args$gene_selector) {
+                my_genes <- get_features(getGenes(cuff, args$genes), args$features)
+            } else {
+                my_genes <- genes(cuff)
+            }
+            csScatter(my_genes, args$x, args$y, smooth = args$smooth, logMode = args$log10)
+        } else if (args$plotType == "volcano") {
+            if (args$gene_selector) {
+                my_genes <- get_features(getGenes(cuff, args$genes), args$features)
+            } else {
+                my_genes <- genes(cuff)
+            }
+            csVolcano(my_genes, args$x, args$y)
+        } else if (args$plotType == "heatmap") {
+            if (args$gene_selector) {
+                my_genes <- getGenes(cuff, args$genes)
+            } else {
+                my_genes <- getGenes(cuff, annotation(genes(cuff))[[1]])
+            }
+            csHeatmap(get_features(my_genes, args$features), clustering = args$clustering, labCol = args$labcol, labRow = args$labrow, border = args$border, logMode = args$log10)
+        } else if (args$plotType == "cluster") {
+            my_genes <- getGenes(cuff, args$genes)
+            csCluster(get_features(my_genes, args$features), k = args$k)
+        } else if (args$plotType == "dispersion") {
+            dispersionPlot(genes(cuff))
+        } else if (args$plotType == "fpkmSCV") {
+            fpkmSCVPlot(genes(cuff))
+        } else if (args$plotType == "scatterMatrix") {
+            csScatterMatrix(genes(cuff))
+        } else if (args$plotType == "expressionplot") {
             my_genes <- getGenes(cuff, args$genes)
-        } else {
-            my_genes <- getGenes(cuff, annotation(genes(cuff))[[1]])
+            expressionPlot(get_features(my_genes, args$features), drawSummary = args$summary, showErrorbars = args$error_bars, replicates = args$replicates)
+        } else if (args$plotType == "expressionbarplot") {
+            my_gene_id <- args$genes
+            my_genes <- getGenes(cuff, my_gene_id)
+            expressionBarplot(get_features(my_genes, args$features), showErrorbars = args$error_bars, replicates = args$replicates)
+        } else if (args$plotType == "mds") {
+            MDSplot(genes(cuff), replicates = args$replicates)
+        } else if (args$plotType == "pca") {
+            PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
+        } else if (args$plotType == "maplot") {
+            MAplot(genes(cuff), args$x, args$y, useCount = args$count)
+        } else if (args$plotType == "genetrack") {
+            my_gene <- getGene(cuff, args$genes)
+            plotTracks(makeGeneRegionTrack(my_gene))
         }
-        csHeatmap(get_features(my_genes, args$features), clustering = args$clustering, labCol = args$labcol, labRow = args$labrow, border = args$border, logMode = args$log10)
-    } else if (args$plotType == "cluster") {
-        my_genes <- getGenes(cuff, args$genes)
-        csCluster(get_features(my_genes, args$features), k = args$k)
-    } else if (args$plotType == "dispersion") {
-        dispersionPlot(genes(cuff))
-    } else if (args$plotType == "fpkmSCV") {
-        fpkmSCVPlot(genes(cuff))
-    } else if (args$plotType == "scatterMatrix") {
-        csScatterMatrix(genes(cuff))
-    } else if (args$plotType == "expressionplot") {
-        my_genes <- getGenes(cuff, args$genes)
-        expressionPlot(get_features(my_genes, args$features), drawSummary = args$summary, showErrorbars = args$error_bars, replicates = args$replicates)
-    } else if (args$plotType == "expressionbarplot") {
-        my_gene_id <- args$genes
-        my_genes <- getGenes(cuff, my_gene_id)
-        expressionBarplot(get_features(my_genes, args$features), showErrorbars = args$error_bars, replicates = args$replicates)
-    } else if (args$plotType == "mds") {
-        MDSplot(genes(cuff), replicates = args$replicates)
-    } else if (args$plotType == "pca") {
-        PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
-    } else if (args$plotType == "maplot") {
-        MAplot(genes(cuff), args$x, args$y, useCount = args$count)
-    } else if (args$plotType == "genetrack") {
-        my_gene <- getGene(cuff, args$genes)
-        plotTracks(makeGeneRegionTrack(my_gene))
+    },
+    error = function(e) {
+        write(paste("Failed:", e, sep = " "), stderr())
+        q("no", 1, TRUE)
     }
-}, error = function(e) {
-    write(paste("Failed:", e, sep = " "), stderr())
-    q("no", 1, TRUE)
-})
+)
 devname <- dev.off()
 print("cummeRbund finished")

tools/cummerbund/cummeRbund.xml

@@ -1,15 +1,18 @@
 <?xml version="1.0"?>
-<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">
+<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy0" profile="24.0">
     <description>visualize Cuffdiff output</description>
     <macros>
         <import>cummeRbund_macros.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
-        <requirement type="package" version="1.0.4">r-argparse</requirement>
-        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="2.0.1">r-argparse</requirement>
+        <requirement type="package" version="3.5.1">r-base</requirement>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
     </requirements>
+    <required_files>
+        <include path="cummeRbund.R" />
+    </required_files>
     <code file="cummeRbund_options.py"/>
     <command detect_errors="aggressive">
 <![CDATA[
@@ -111,8 +114,8 @@
                     <expand macro="multiple_genes_conditional" />
                 </when>
                 <when value="volcano">
-                    <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
-                    <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
+                    <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.get_file_name())" />
+                    <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.get_file_name())" />
                     <expand macro="multiple_genes_conditional" />
                 </when>
                 <when value="heatmap">
@@ -144,15 +147,15 @@
                 <when value="scatterMatrix" />
                 <when value="expressionplot">
                     <expand macro="features_selector" />
-                    <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
+                    <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.get_file_name())" />
                     <param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
                     <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
                     <expand macro="replicates_checkbox" />
                     <expand macro="log10_checkbox" />
                 </when>
                 <when value="expressionbarplot">
                     <expand macro="features_selector" />
-                    <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
+                    <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.get_file_name())" />
                     <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
                     <expand macro="replicates_checkbox" />
                     <expand macro="log10_checkbox" />
@@ -179,7 +182,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
+                <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -195,7 +198,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
+                <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -209,7 +212,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
+                <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -223,7 +226,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
+                <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -237,7 +240,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
+                <discovered_dataset designation="pca-0" ftype="png" file="pca.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -253,7 +256,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
+                <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -269,7 +272,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
+                <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -289,7 +292,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
+                <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -303,7 +306,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="density-0" ftype="png" file="density.png" />
+                <discovered_dataset designation="density-0" ftype="png" file="density.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -317,7 +320,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
+                <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -333,7 +336,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
+                <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -347,7 +350,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
+                <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" compare="sim_size" />
             </output>
         </test>
         <test>
@@ -361,7 +364,7 @@
             </repeat>
             <output name="output" ftype="txt">
                 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
-                <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
+                <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" compare="sim_size" />
             </output>
         </test>
     </tests>

tools/cummerbund/cummeRbund_macros.xml

@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.16.0</token>
+    <token name="@TOOL_VERSION@">2.24.0</token>
     <macro name="replicates_checkbox">
         <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
     </macro>
     <macro name="log10_checkbox">
         <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
     </macro>
     <macro name="xy_selector">
-        <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
-        <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
+        <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.get_file_name())" />
+        <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.get_file_name())" />
     </macro>
     <macro name="genes_selector">
         <repeat name="genes" title="Genes" min="2">
             <!-- Cannot create a heatmap for less than two genes -->
-            <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
+            <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.get_file_name())" />
         </repeat>
     </macro>
     <macro name="features_selector">