| Previous changeset 0:2f7381ee5235 (2015-06-30) |
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Commit message:
planemo upload |
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modified:
abims_hclustering.r abims_hclustering.xml |
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added:
Makefile |
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removed:
static/images/anova_filtered.png static/images/anova_pvalue.png static/images/pca_abims_Rplots.png static/images/pca_abims_Rplots1.png static/images/pca_abims_eigenvalue.png static/images/pca_abims_percentage_of_variance.png |
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| diff -r 2f7381ee5235 -r 36fc0a87d7fb Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Nov 13 08:43:11 2015 -0500 |
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| @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=hclustering.tgz +DEP=abims_hclustering.r abims_hclustering.xml static + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz + |
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| diff -r 2f7381ee5235 -r 36fc0a87d7fb abims_hclustering.r --- a/abims_hclustering.r Tue Jun 30 06:36:09 2015 -0400 +++ b/abims_hclustering.r Fri Nov 13 08:43:11 2015 -0500 |
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| @@ -21,10 +21,23 @@ # -- Normalization: logratio -- if (normalization) { - #meandata = apply(data,1,mean, na.rm=T) - #data = log2(data/meandata) - data=t(scale(t(data))) + #meandata = apply(data,1,mean, na.rm=T) + #data = log2(data/meandata) + data=t(scale(t(data))) + + #AMAP: Unable to compute Hierarchical Clustering: missing values in distance matrix + #Erreur dans hcluster(x, method = method, link = link) : + # Missing values in distance Matrix + #Calls: do.call -> <Anonymous> -> hclust2treeview -> hcluster + #Exécution arrêtée + data[is.nan(data)] = 0 } + + #Erreur dans `[.default`(xj, i) : + # les indices négatifs ne peuvent être mélangés qu'à des 0 + #Calls: do.call ... r2cdt -> [ -> [.data.frame -> [ -> [.factor -> NextMethod + #Exécution arrêtée + data = data[!apply(data,1,sum)==0,] # -- hclust / output files for TreeView -- file="hclust.cdt" |
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| diff -r 2f7381ee5235 -r 36fc0a87d7fb abims_hclustering.xml --- a/abims_hclustering.xml Tue Jun 30 06:36:09 2015 -0400 +++ b/abims_hclustering.xml Fri Nov 13 08:43:11 2015 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1"> +<tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1.2"> <description>using ctc R package for java-treeview</description> - <command interpreter="Rscript"> - abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec" - </command> + <command interpreter="Rscript"><![CDATA[ + abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec" && mv hclust.zip $outputzip + ]]></command> <inputs> <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> @@ -50,14 +50,14 @@ </inputs> <outputs> - <data name="hclust_zip" format="zip" from_work_dir="hclust.zip" label="${input.name[:-4]}.hclust.zip" /> + <data name="outputzip" format="zip" label="${input.name[:-4]}.heatmap.zip for Java Treeview" /> </outputs> <stdio> <exit_code range="1:" level="fatal" /> </stdio> - <help> + <help><![CDATA[ @@ -102,6 +102,35 @@ +----------------- +Workflow position +----------------- + + +**Upstream tools** + ++---------------------------+----------------------------------------+--------+------------------------+ +| Name | Output file | Format | parameter | ++===========================+========================================+========+========================+ +|xcms.diffreport |xset.diffreport.data_matrix.tsv | Tabular| Data table file | ++---------------------------+----------------------------------------+--------+------------------------+ +|CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file | ++---------------------------+----------------------------------------+--------+------------------------+ +|Anova |xset.anova_filtered.tabular | Tabular| Data table file | ++---------------------------+----------------------------------------+--------+------------------------+ + + + +**Downstream tools** + ++---------------------------+-----------------------------------------------+---------------------+ +| Name | Output file | Format | ++===========================+===============================================+=====================+ +|Treeview (out of Galaxy) | cdt,gtr and atr files needed for Java Treeview|Java Treeview formats| ++---------------------------+-----------------------------------------------+---------------------+ + + + ----------- Input files ----------- @@ -126,6 +155,7 @@ Note however, that methods median and centroid are not leading to a monotone distance measure, or equivalently the resulting dendrograms can have so called inversions (which are hard to interpret). + ------------ Output files ------------ @@ -160,7 +190,7 @@ +--------+------------------+----------------+ -| Name | Bur-eH_FSP_102 | Bur-eH_FSP_22 | +| Name | Bur-eH_FSP_102 | Bur-eH_FSP_22 | +========+==================+================+ |M202T601| 91206595.7559783 |106808979.08546 | +--------+------------------+----------------+ @@ -189,4 +219,4 @@ </help> -</tool> +]]></tool> |
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