diff heatmap2.xml @ 7:53460afd5115 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe

--- a/heatmap2.xml	Wed Apr 13 09:34:26 2022 +0000
+++ b/heatmap2.xml	Wed Mar 08 14:11:15 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="ggplot2_heatmap2" name="heatmap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="ggplot2_heatmap2" name="heatmap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <macros>
-        <token name="@TOOL_VERSION@">3.1.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">3.1.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">r-gplots</requirement>
@@ -53,21 +53,25 @@
     scale <- "$zscore_cond.scale"
 #end if
 
-srtCol <- 45
+srtCol <- 30
 #if $labels == "both"
     rlabs <- NULL
     clabs <- NULL
+    label_margins <- c(8,8)
 #elif $labels == "rows"
     rlabs <- NULL
     clabs <- FALSE
     srtCol <- NULL
+    label_margins <- c(1,8)
 #elif $labels == "columns"
     rlabs <- FALSE
     clabs <- NULL
+    label_margins <- c(8,1)
 #elif $labels == "none"
     rlabs <- FALSE
     clabs <- FALSE
     srtCol <- NULL
+    label_margins <- c(1,1)
 #end if
 
 #if $cluster_cond.cluster == "yes":
@@ -75,12 +79,24 @@
     #if $cluster_cond.cluster_cols_rows == "both"
         reorder_cols <- TRUE
         reorder_rows <- TRUE
+        layout_matrix <- rbind(c(4,3), c(2,1))
+        key_margins <- list(mar=c(4,0.5,2,1))
+        lheight <- c(1, 5)
+        lwidth <- c(1,3)
     #elif $cluster_cond.cluster_cols_rows == "row"
         reorder_cols <- FALSE
         reorder_rows <- TRUE
+        layout_matrix <- rbind(c(3,4), c(2,1))
+        key_margins <- list(mar=c(3,5,1,10))
+        lheight <- c(1,7)
+        lwidth <- c(1,3)
     #elif $cluster_cond.cluster_cols_rows == "column"
         reorder_cols <- TRUE
         reorder_rows <- FALSE
+        layout_matrix <- rbind(c(4), c(3), c(1), c(2))
+        key_margins <- list(mar=c(4,0.5,2,1))
+        lheight <- c(0.3, 2, 6, 1)
+        lwidth <- c(1)
     #end if
     hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
     #if $cluster_cond.distance == 'pearson_correlation':
@@ -94,8 +110,13 @@
     dendrogramtoplot <- "none"
     reorder_cols <- FALSE
     reorder_rows <- FALSE
+    layout_matrix <- rbind(c(0,4,3), c(0,1,2))
+    key_margins <- list(mar=c(3,5,1,10))
+    lheight <- c(1,7)
+    lwidth <- c(1,7,1)
     hclust_fun <- hclust
     dist_fun <- dist
+    label_margins <- c(8,2)
 #end if
 
 ncolors <- 50
@@ -110,13 +131,15 @@
 #if $image_file_format == "pdf":
     pdf(file='$output1')
 #else:
-    png(file='$output1')
+    png(file='$output1', res=240, height=2000, width=2000)
 #end if
 
 heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
     distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
-    col=colused, trace="none", density.info = "none", margins=c(8,8),
-    main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=srtCol)
+    col=colused, trace="none", density.info = "none", margins=label_margins,
+    main = '$title', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
+    keysize=3, key.xlab='$key', key.title='', key.par=key_margins,
+    lmat=layout_matrix, lhei=lheight, lwid=lwidth)
 
 dev.off()
         ]]></configfile>
@@ -128,7 +151,7 @@
         <param name="title" type="text" format="txt" label="Plot title"/>
         <param name="key" type="text" format="txt" label="key title"/>
         <param name="transform" type="select" label="Data transformation">
-            <option value="none">Plot the data as it is</option>
+            <option value="none" selected="true">Plot the data as it is</option>
             <option value="log2">Log2(value) transform my data</option>
             <option value="log2plus1">Log2(value+1) transform my data</option>
             <option value="log10">Log10(value) transform my data</option>
@@ -136,7 +159,7 @@
         </param>
         <conditional name="zscore_cond">
             <param name="zscore" type="select" label="Compute z-scores prior to clustering">
-                <option value="none">Do not compute z-scores</option>
+                <option value="none" selected="true">Do not compute z-scores</option>
                 <option value="rows">Compute on rows</option>
                 <option value="cols">Compute on columns</option>
             </param>
@@ -152,7 +175,7 @@
         </conditional>
         <conditional name="cluster_cond">
             <param name="cluster" type="select" label="Enable data clustering">
-                <option value="yes">Yes</option>
+                <option value="yes" selected="true">Yes</option>
                 <option value="no">No</option>
             </param>
             <when value="yes">
@@ -192,7 +215,7 @@
         </param>
         <conditional name="colorchoice">
             <param name="type" type="select" label="Type of colormap to use">
-                <option value="palettes">RColorBrewer palettes</option>
+                <option value="palettes" selected="true">RColorBrewer palettes</option>
                 <option value="two">Gradient with 2 colors</option>
                 <option value="three">Gradient with 3 colors</option>
             </param>
@@ -238,7 +261,7 @@
             </when>
         </conditional>
         <param name="image_file_format" type="select" label="Output format">
-            <option value="pdf">PDF</option>
+            <option value="pdf" selected="true">PDF</option>
             <option value="png">PNG</option>
         </param>
     </inputs>
@@ -311,5 +334,11 @@
 Input data should have row labels in the first column and column labels. For example, the row labels (the first column) should represent gene IDs and the column labels should represent sample IDs.
     ]]></help>
     <citations>
+        <citation type="bibtex">
+            @ONLINE{heatmap2,
+                title = {heatmap.2: Enhanced Heat Map},
+                url = {https://rdocumentation.org/packages/gplots/versions/3.1.3/topics/heatmap.2}
+            }
+        </citation>
     </citations>
 </tool>