| Previous changeset 9:51c6ccaace7e (2024-10-11) Next changeset 11:6a097d09fca3 (2025-12-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a |
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modified:
heatmap2.xml test-data/result1.pdf test-data/result1pearson.pdf test-data/result2.png test-data/result3.png test-data/result4.png test-data/result5.png test-data/result6.png |
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added:
test-data/result7.png |
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| diff -r 51c6ccaace7e -r 48b42ee61bc5 heatmap2.xml --- a/heatmap2.xml Fri Oct 11 13:12:37 2024 +0000 +++ b/heatmap2.xml Tue Nov 12 16:44:40 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="ggplot2_heatmap2" name="heatmap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> <macros> <token name="@TOOL_VERSION@">3.2.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-gplots</requirement> @@ -79,6 +79,9 @@ #if $cluster_cond.cluster_cols_rows == "both" reorder_cols <- TRUE reorder_rows <- TRUE + # Layout is: + # 4 = color key | 3 = dendrogram for columns + # 2 = dendrogram for rows | 1 = heatmap layout_matrix <- rbind(c(4,3), c(2,1)) key_margins <- list(mar=c(4,0.5,2,1)) lheight <- c(1, 5) @@ -86,6 +89,9 @@ #elif $cluster_cond.cluster_cols_rows == "row" reorder_cols <- FALSE reorder_rows <- TRUE + # Layout is: + # 3 = dendrogram for columns (not plotted) + title | 4 = color key + # 2 = dendrogram for rows | 1 = heatmap layout_matrix <- rbind(c(3,4), c(2,1)) key_margins <- list(mar=c(3,5,1,10)) lheight <- c(1,7) @@ -93,10 +99,14 @@ #elif $cluster_cond.cluster_cols_rows == "column" reorder_cols <- TRUE reorder_rows <- FALSE - layout_matrix <- rbind(c(4), c(3), c(1), c(2)) - key_margins <- list(mar=c(4,0.5,2,1)) - lheight <- c(0.3, 2, 6, 1) - lwidth <- c(1) + # Layout is: + # nothing | 4 = color key + # nothing | 3 = dendrogram for columns + # 2 = dendrogram for rows (not plotted) | 1 = heatmap + layout_matrix <- rbind(c(0, 4), c(0, 3), c(2, 1)) + key_margins <- list(mar=c(1, 5, 1, 10)) + lheight <- c(0.5, 1, 5) + lwidth <- c(0.01, 1) #end if hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering') #if $cluster_cond.distance == 'pearson_correlation': @@ -283,7 +293,7 @@ <param name="input1" value="mtcars.txt"/> <param name="cluster" value="no"/> <param name="image_file_format" value="png"/> - <output name="output1" file="result2.png" compare="sim_size" delta="12000" /> + <output name="output1" file="result2.png" compare="image_diff" /> </test> <test> <param name="input1" value="mtcars.txt"/> @@ -293,7 +303,7 @@ <param name="labels" value="rows"/> <param name="type" value="three"/> <param name="image_file_format" value="png"/> - <output name="output1" file="result3.png" compare="sim_size"/> + <output name="output1" file="result3.png" compare="image_diff"/> </test> <test> <param name="input1" value="mtcars.txt"/> @@ -307,7 +317,7 @@ <param name="zscore" value="rows"/> <param name="type" value="three"/> <param name="image_file_format" value="png"/> - <output name="output1" file="result4.png" compare="sim_size" delta="12000" /> + <output name="output1" file="result4.png" compare="image_diff" /> </test> <test> <param name="input1" value="mtcars.txt"/> @@ -316,7 +326,7 @@ <param name="scale" value="row"/> <param name="type" value="three"/> <param name="image_file_format" value="png"/> - <output name="output1" file="result5.png" compare="sim_size" delta="12000" /> + <output name="output1" file="result5.png" compare="image_diff" /> </test> <test> <param name="input1" value="mtcars.txt"/> @@ -325,7 +335,18 @@ <param name="scale" value="column"/> <param name="type" value="three"/> <param name="image_file_format" value="png"/> - <output name="output1" file="result6.png" compare="sim_size" delta="12000" /> + <output name="output1" file="result6.png" compare="image_diff" /> + </test> + <test> + <param name="input1" value="mtcars.txt"/> + <param name="cluster" value="yes"/> + <param name="cluster_cols_rows" value="column"/> + <param name="distance" value="pearson_correlation"/> + <param name="scale" value="row"/> + <param name="type" value="palettes"/> + <param name="name" value="YlOrBr"/> + <param name="image_file_format" value="png"/> + <output name="output1" file="result7.png" compare="image_diff" /> </test> </tests> <help><
