# HG changeset patch
# User lecorguille
# Date 1491220429 14400
# Node ID 3a53e63555c706681faa7d9ae6183287c0918c08
# Parent  5cc59ee748b6755ebadb24c8560dd7b5a4324fbc
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767

diff -r 5cc59ee748b6 -r 3a53e63555c7 abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Wed Mar 22 16:07:25 2017 -0400
+++ b/abims_xcms_summary.xml	Mon Apr 03 07:53:49 2017 -0400
@@ -57,6 +57,28 @@
 
 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
 
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ================= ===================== ==========
+Name                      output file       format                parameter
+========================= ================= ===================== ==========
+xcms.xcmsSet              xset.RData        rdata.xcms.raw        RData file
+------------------------- ----------------- --------------------- ----------
+xcms.group                xset.RData        rdata.xcms.group      RData file
+------------------------- ----------------- --------------------- ----------
+xcms.retcor               xset.RData        rdata.xcms.retcor     RData file
+------------------------- ----------------- --------------------- ----------
+xcms.fillpeaks            xset.RData        rdata.xcms.fillpeaks  RData file
+------------------------- ----------------- --------------------- ----------
+CAMERA.annotate           xset.RData        rdata.camera.*        RData file
+========================= ================= ===================== ==========
+
+
+.. image:: xcms_merge_workflow.png
 
 ---------------------------------------------------
 
diff -r 5cc59ee748b6 -r 3a53e63555c7 macros.xml
--- a/macros.xml	Wed Mar 22 16:07:25 2017 -0400
+++ b/macros.xml	Mon Apr 03 07:53:49 2017 -0400
@@ -107,11 +107,11 @@
         </conditional>
     </xml>
 
-    <xml name="output_peaklist">
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
+    <xml name="output_peaklist"  token_function="">
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
             <filter>(peaklist['peaklistBool'])</filter>
         </data>
-        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
+        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
             <filter>(peaklist['peaklistBool'])</filter>
         </data>
     </xml>
diff -r 5cc59ee748b6 -r 3a53e63555c7 static/images/xcms_summary_workflow.png
Binary file static/images/xcms_summary_workflow.png has changed
diff -r 5cc59ee748b6 -r 3a53e63555c7 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html
--- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Wed Mar 22 16:07:25 2017 -0400
+++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Mon Apr 03 07:53:49 2017 -0400
@@ -19,7 +19,7 @@
 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
 <tr> <td> ko15 </td> <td> ./ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> ./ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> ./wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> ./wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
 </table>
-<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>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.
 </div>
 <h2>Function launched:</h2>
 <div><table>
diff -r 5cc59ee748b6 -r 3a53e63555c7 test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html
--- a/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html	Wed Mar 22 16:07:25 2017 -0400
+++ b/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html	Mon Apr 03 07:53:49 2017 -0400
@@ -19,7 +19,7 @@
 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
 <tr> <td> ko15 </td> <td> faahKO_reduce/KO/ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> faahKO_reduce/KO/ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> faahKO_reduce/WT/wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> faahKO_reduce/WT/wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
 </table>
-<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>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.
 </div>
 <h2>Function launched:</h2>
 <div><table>
diff -r 5cc59ee748b6 -r 3a53e63555c7 xcms_summary.r
--- a/xcms_summary.r	Wed Mar 22 16:07:25 2017 -0400
+++ b/xcms_summary.r	Mon Apr 03 07:53:49 2017 -0400
@@ -93,11 +93,11 @@
         } 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."
+            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 changed 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>")
-            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/>"
+            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 changed during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
         }
 
         writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")