# HG changeset patch
# User lecorguille
# Date 1447422191 18000
# Node ID 36fc0a87d7fb1b2a32b2aa93ef9dd7fe8ecceebc
# Parent  2f7381ee5235df3ba162d580f048e263c437890c
planemo upload

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
@@ -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
+
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
@@ -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"
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
@@ -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>
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/anova_filtered.png
Binary file static/images/anova_filtered.png has changed
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/anova_pvalue.png
Binary file static/images/anova_pvalue.png has changed
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/pca_abims_Rplots.png
Binary file static/images/pca_abims_Rplots.png has changed
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/pca_abims_Rplots1.png
Binary file static/images/pca_abims_Rplots1.png has changed
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/pca_abims_eigenvalue.png
Binary file static/images/pca_abims_eigenvalue.png has changed
diff -r 2f7381ee5235 -r 36fc0a87d7fb static/images/pca_abims_percentage_of_variance.png
Binary file static/images/pca_abims_percentage_of_variance.png has changed