# HG changeset patch
# User recetox
# Date 1612438499 0
# Node ID 08b09930cd734454b1032983d32707800f8173f0
# Parent d9c9ec0e2bd814bb1a9ae04fa9aec18cfdc5cf86
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit beda1b99934fb8254de04bb38e41eb9ce836d71d"
diff -r d9c9ec0e2bd8 -r 08b09930cd73 ramclustr_csv.xml
--- a/ramclustr_csv.xml Wed Jan 13 11:42:34 2021 +0000
+++ b/ramclustr_csv.xml Thu Feb 04 11:34:59 2021 +0000
@@ -57,6 +57,39 @@
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Documentation
For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
diff -r d9c9ec0e2bd8 -r 08b09930cd73 test-data/csv_test-input.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csv_test-input.csv Thu Feb 04 11:34:59 2021 +0000
@@ -0,0 +1,4 @@
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diff -r d9c9ec0e2bd8 -r 08b09930cd73 test-data/metadata_csv.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata_csv.txt Thu Feb 04 11:34:59 2021 +0000
@@ -0,0 +1,6 @@
+Raw mass spectrometry data were processed using an R based workflow for feature detection, retention time alignment, feature grouping, peak filling, feature clustering. Feature data was input as .csv files with ramclustR parameter settings of st = 5 sr = 0.5 and maxt = 1.RAMClustR (version 1.1.0) was utilized to cluster features into spectra (Broeckling 2014). The feature similarity matrix was clustered using fastcluster package heirarchical clustering method using the average method. The dendrogram was cut using the cutreeDynamicTree function from the dynamicTreeCut package. Cutting parameters were set to minModuleSize = 2, hmax = 0.3, and deepSplit = FALSE.
+
+ 203 features were collapsed into 22 spectra. Since there were fewer than five injections, clustering was performed only using retention time simiilarity.
+
+(Broeckling 2014): Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014. 86(14):6812-7.
+
diff -r d9c9ec0e2bd8 -r 08b09930cd73 test-data/ramclustR-csv_object.RData
Binary file test-data/ramclustR-csv_object.RData has changed
diff -r d9c9ec0e2bd8 -r 08b09930cd73 test-data/spec-abundance_csv.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spec-abundance_csv.csv Thu Feb 04 11:34:59 2021 +0000
@@ -0,0 +1,4 @@
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diff -r d9c9ec0e2bd8 -r 08b09930cd73 test-data/test-spectra_csv.msp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-spectra_csv.msp Thu Feb 04 11:34:59 2021 +0000
@@ -0,0 +1,357 @@
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