Mercurial > repos > lecorguille > xcms_merge
changeset 2:3a5204f14fff draft
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(-) [+] |
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--- /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