changeset 4:1245c04eebde draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 17:07:53 2016 -0500
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=xcms_summary.tgz
+DEP=abims_xcms_summary.xml xcms_summary.r tool_dependencies.xml repository_dependencies.xml test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 17:07:53 2016 -0500
@@ -0,0 +1,8 @@
+
+Changelog/News
+--------------
+
+**Version 1.0.0 - 10/02/2016**
+
+- NEW: Create a summary of XCMS analysis
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh	Mon Feb 22 17:07:53 2016 -0500
@@ -0,0 +1,1 @@
+planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics"

--- a/xcms_summary.r	Fri Feb 19 11:51:18 2016 -0500
+++ b/xcms_summary.r	Mon Feb 22 17:07:53 2016 -0500
@@ -42,7 +42,7 @@
 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
 
 # retrocompatability
-if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))
+if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset)))
 
 if (!exists("xset")) stop("You need at least a xset or a xa object.")
 
@@ -77,7 +77,7 @@
 
     writehtml("<h2>Samples used:</h2>")
     writehtml("<div><table>")
-        if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) {
+        if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) {
             sampleNameHeaderHtml = paste("<th>sample</th>")
             sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
         } else {
@@ -89,13 +89,13 @@
             md5sumHeaderHtml = ""
             md5sumHtml = ""
             md5sumLegend=""
-        } else if (is.null(md5sumList$removalBadCharacters)) {
+        } else if (!is.null(md5sumList$removalBadCharacters)) {
             md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
             md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
             md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process."
         } else {
             md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
-            md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
+            md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>")
             md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
         }