Mercurial > repos > lecorguille > xcms_merge

changeset 2:3a5204f14fff draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:48:41 -0500
parents 090cf284d9ff
children f439ed7a8f03
files README.rst test-data/sampleMetadata_missing.tab xcms_merge.xml
diffstat 3 files changed, 39 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Feb 13 04:48:41 2018 -0500
@@ -0,0 +1,13 @@
+
+Changelog/News
+--------------
+
+**Version 1.0.1 - 13/02/2017**
+
+- IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
+
+
+**Version 1.0.0 - 03/02/2017**
+
+- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata_missing.tab	Tue Feb 13 04:48:41 2018 -0500
@@ -0,0 +1,5 @@
+wt16	WT
+wt15	WT
+ko15	KO
+ko10	KO
+foobar01	FOOBAR
--- a/xcms_merge.xml	Wed Nov 29 09:45:39 2017 -0500
+++ b/xcms_merge.xml	Tue Feb 13 04:48:41 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0">
+<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0">
     <description>Merge xcms.xcmsSet xset in one to be used by group</description>
 
     <macros>
@@ -60,6 +60,13 @@
     }
 
     sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]
+
+    if (any(is.na(sampclass(xset)))) {
+        sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))]
+        error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
+        print(error_message)
+        stop(error_message)
+    }
 #end if
 
 
@@ -123,6 +130,14 @@
                 <has_text text="Sample classes: ." />
             </assert_stdout>
         </test>
+        <test expect_failure="True">
+            <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
+            <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
+            <expand macro="test_file_load_single"/>
+            <assert_stderr>
+                <has_text text="Those samples are missing in your sampleMetadata: ko16" />
+            </assert_stderr>
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -215,6 +230,11 @@
 Changelog/News
 --------------
 
+**Version 1.0.1 - 13/02/2017**
+
+- IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
+
+
 **Version 1.0.0 - 03/02/2017**
 
 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group