Mercurial > repos > iuc > edger
changeset 7:47094543a5ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
| author | iuc |
|---|---|
| date | Thu, 08 Aug 2019 06:43:49 -0400 |
| parents | 7cf6248bc173 |
| children | ea85027d986c |
| files | edger.xml test-data/matrix-complex.txt |
| diffstat | 2 files changed, 39 insertions(+), 3 deletions(-) [+] |
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--- a/edger.xml Sat Feb 09 07:19:54 2019 -0500 +++ b/edger.xml Thu Aug 08 06:43:49 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="edger" name="edgeR" version="3.24.1"> +<tool id="edger" name="edgeR" version="3.24.1+galaxy1"> <description> Perform differential expression of count data </description> @@ -175,9 +175,9 @@ <!-- Contrasts --> <repeat name="rep_contrast" title="Contrast" min="1" default="1"> - <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> + <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (MT.t1-MT.t0)-(WT.t1-WT.t0). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons."> <validator type="empty_field" /> - <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator> + <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator> </param> </repeat> @@ -309,6 +309,35 @@ </assert_contents> </output> </test> + <!-- Complex contrasts constructions --> + <test> + <param name="format" value="matrix" /> + <param name="counts" value="matrix-complex.txt" /> + <repeat name="rep_factor"> + <param name="factorName" value="Genotype"/> + <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB" /> + </repeat> + <repeat name="rep_contrast"> + <param name="contrast" value="(MutA-MutB)-(WTA-WTB)" /> + </repeat> + <param name="normalisationOption" value="TMM" /> + <output_collection name="outTables" count="1"> + <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular" > + <assert_contents> + <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> + <has_text_matching expression="11304.*15.53" /> + </assert_contents> + </element> + </output_collection> + <output name="outReport" > + <assert_contents> + <has_text text="edgeR Analysis Output" /> + <has_text text="quasi-likelihood" /> + <not_has_text text="likelihood ratio" /> + <not_has_text text="RData" /> + </assert_contents> + </output> + </test> <!-- Ensure annotation file input works --> <test> <param name="format" value="matrix" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/matrix-complex.txt Thu Aug 08 06:43:49 2019 -0400 @@ -0,0 +1,7 @@ +GeneID MutA1 MutA2 MutA3 MutB1 MutB2 MutB3 WTA1 WTA2 WTA3 WTB1 WTB2 WTB3 +11287 1463 1441 1495 1463 1441 1495 1699 1528 1601 1699 1528 1601 +11298 1345 1291 1346 1345 1291 1346 1905 1744 1834 1905 1744 1834 +11302 5 6 5 5 6 5 6 8 7 6 8 7 +11303 1574 1519 1654 1574 1519 1654 2099 1974 2100 2099 1974 2100 +11304 361 397 346 361 397 346 356 312 337 356 312 337 +11305 1762 1942 2027 1762 1942 2027 2528 2438 2493 2528 2438 2493