| Previous changeset 4:ca7cb0eaad62 (2019-02-11) Next changeset 6:566197475670 (2022-04-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d" |
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modified:
heatmap2.xml |
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added:
test-data/result1pearson.pdf test-data/result2.png test-data/result3.png |
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removed:
test-data/result2.pdf |
| b |
| diff -r ca7cb0eaad62 -r 3b37b1b1c3a7 heatmap2.xml --- a/heatmap2.xml Mon Feb 11 17:32:28 2019 -0500 +++ b/heatmap2.xml Tue Apr 12 15:53:40 2022 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@">\n <macros>\n- <token name="@VERSION@">3.0.1</token>\n+ <token name="@VERSION@">3.1.1</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">r-gplots</requirement>\n- <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n+ <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n cat \'$script\' &&\n@@ -39,63 +39,91 @@\n linput <- log10(mat_input+1)\n #end if\n \n-#if $colorscheme == "whrd"\n- colorscale = colfunc <- colorRampPalette(c("white", "red"))\n-#elif $colorscheme == "whblu"\n- colorscale = colfunc <- colorRampPalette(c("white", "blue"))\n-#elif $colorscheme == "blwhre"\n- colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))\n+#if $zscore_cond.zscore == "rows":\n+ linput <- t(apply(linput, 1, scale))\n+ colnames(linput) <- colnames(input)\n+ rownames(linput) <- input[,1]\n+ scale <- "none"\n+#elif $zscore_cond.zscore == "cols":\n+ linput <- apply(linput, 2, scale)\n+ rownames(linput) <- input[,1]\n+ scale <- "none"\n+#elif $zscore_cond.zscore == "none":\n+ scale <- "$zscore_cond.scale"\n #end if\n \n-#if $labels== "both"\n- rlabs = NULL\n- clabs = NULL\n-#elif $labels== "rows"\n- rlabs = NULL\n- clabs = FALSE\n-#elif $labels== "columns"\n- rlabs = FALSE\n- clabs = NULL\n-#elif $labels== "none"\n- rlabs = FALSE\n- clabs = FALSE\n+srtCol <- 45\n+#if $labels == "both"\n+ rlabs <- NULL\n+ clabs <- NULL\n+#elif $labels == "rows"\n+ rlabs <- NULL\n+ clabs <- FALSE\n+ srtCol <- NULL\n+#elif $labels == "columns"\n+ rlabs <- FALSE\n+ clabs <- NULL\n+#elif $labels == "none"\n+ rlabs <- FALSE\n+ clabs <- FALSE\n+ srtCol <- NULL\n #end if\n \n-pdf(file=\'$output1\')\n-colorscale\n+#if $cluster_cond.cluster == "yes":\n+ dendrogramtoplot <- "$cluster_cond.cluster_cols_rows"\n+ #if $cluster_cond.cluster_cols_rows == "both"\n+ reorder_cols <- TRUE\n+ reorder_rows <- TRUE\n+ #elif $cluster_cond.cluster_cols_rows == "row"\n+ reorder_cols <- FALSE\n+ reorder_rows <- TRUE\n+ #elif $cluster_cond.cluster_cols_rows == "column"\n+ reorder_cols <- TRUE\n+ reorder_rows <- FALSE\n+ #end if\n+ hclust_fun <- function(x) hclust(x, method=\'$cluster_cond.clustering\')\n+ #if $cluster_cond.distance == \'pearson_correlation\':\n+ dist_fun <- function(x) as.dist(1 - cor(t(x)))\n+ #elif $cluster_cond.distance == \'spearmann_correlation\':\n+ dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman"))\n+ #else:\n+ dist_fun <- function(x) dist(x, method=\'$cluster_cond.distance\')\n+ #end if\n+#else:\n+ dendrogramtoplot <- "none"\n+ reorder_cols <- FALSE\n+ reorder_rows <- FALSE\n+ hclust_fun <- hclust\n+ dist_fun <- dist\n+#end if\n \n-#if $cluster_cond.cluster:\n- hclust_fun = function(x) hclust(x, method=\'$cluster_cond.clustering\')\n- dist_fun = function(x) dist(x, method=\'$cluster_cond.distance\')\n- #if $cluster_cond.cluster_cols_rows=="rows":\n- heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE,\n- distfun=dist_fun, hclustfun=hclust_fun, scale = \'$scale\', labRow = rlabs, labCol = clabs,\n- col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),\n- main = \'$title\', key.xlab=\'$key\', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)\n- #elif $cluster_cond.cluster_cols_rows=="columns":\n- heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE,\n- distfun=dist_fun, hclustfun=hclust_fun, scale = \'$scale\', labRow = rlabs, labCol = clabs,\n- col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),\n- main = \'$title\', key.xlab=\'$key\', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)\n- #else\n- heatmap.2(linput,\n- distfun=dist_fun, hclustfun=hc'..b' <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="RdYlGn">RdYlGn</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Blues">Blues</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="PuBuGn">PuBuGn</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="Purples">Purples</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="Reds">Reds</option>\n+ <option value="YlGn">YlGn</option>\n+ <option value="YlGnBu">YlGnBu</option>\n+ <option value="YlOrBr">YlOrBr</option>\n+ <option value="YlOrRd">YlOrRd</option>\n+ </param>\n+ </when>\n+ <when value="two">\n+ <param name="color1" type="color" value="#ffffff" label="First color" />\n+ <param name="color2" type="color" value="#ff0000" label="Second color" />\n+ </when>\n+ <when value="three">\n+ <param name="color1" type="color" value="#0000ff" label="First color" />\n+ <param name="color2" type="color" value="#ffffff" label="Second color" />\n+ <param name="color3" type="color" value="#ff0000" label="Third color" />\n+ </when>\n+ </conditional>\n+ <param name="image_file_format" type="select" label="Output format">\n+ <option value="pdf">PDF</option>\n+ <option value="png">PNG</option>\n </param>\n </inputs>\n <outputs>\n- <data name="output1" format="pdf"/>\n+ <data name="output1" format="pdf">\n+ <change_format>\n+ <when input="image_file_format" value="png" format="png" />\n+ </change_format>\n+ </data>\n </outputs>\n <tests>\n <test>\n <param name="input1" value="mtcars.txt"/>\n- <param name="cluster" value="true"/>\n+ <param name="cluster" value="yes"/>\n+ <param name="type" value="two"/>\n <output name="output1" file="result1.pdf" compare="sim_size"/>\n </test>\n <test>\n <param name="input1" value="mtcars.txt"/>\n- <param name="cluster" value=""/>\n- <output name="output1" file="result2.pdf" compare="sim_size"/>\n+ <param name="cluster" value="no"/>\n+ <param name="image_file_format" value="png"/>\n+ <output name="output1" file="result2.png" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="input1" value="mtcars.txt"/>\n+ <param name="zscore" value="cols"/>\n+ <param name="cluster" value="yes"/>\n+ <param name="cluster_cols_rows" value="row"/>\n+ <param name="labels" value="rows"/>\n+ <param name="type" value="three"/>\n+ <param name="image_file_format" value="png"/>\n+ <output name="output1" file="result3.png" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="input1" value="mtcars.txt"/>\n+ <param name="cluster" value="yes"/>\n+ <param name="distance" value="pearson_correlation"/>\n+ <param name="type" value="two"/>\n+ <output name="output1" file="result1pearson.pdf" compare="sim_size"/>\n </test>\n </tests>\n <help><
