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+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1038289.svg)](https://doi.org/10.5281/zenodo.1038289)
+
+# w4mjoinpn_galaxy_wrapper
+
+This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive 
+ionization-mode and the other in negative ionization-mode, for reasons set forth below.  
+
+Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, http://dx.doi.org/10.1093/bioinformatics/btu813; http://workflow4metabolomics.org; 
+https://github.com/workflow4metabolomics) provides a suite of Galaxy tools for processing and analyzing metabolomics data.
+  
+W4M uses the XCMS package (Smith *et al.*, 2006 http://dx.doi.org/10.1021/ac051437y) to extract features and align 
+their retention times among multiple samples. 
+
+After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012, http://dx.doi.org/10.1021/ac202450g) 
+"to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
+
+Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive)
+because it would not make sense to attempt to use CAMERA otherwise.
+
+However, multivariate analysis in general, and particularly the "False Discovery Rate" adjustment in hypothesis testing,
+would both benefit from having all variables (features), negative and positive, combined for one analysis.  It is also
+cumbersome to be forced to do an analysis twice, once for each ionization mode.
+
+This tool will fail:
+ * when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix
+ * when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata
+
+Otherwise
+  * the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data
+are prefixed with "P"; negative, with "N".
+  * the two variableMetadata files are concatenated, and the names of features are prefixed in the same way.
+  * if sampleMetadata has a polarity column, its value is set to "posneg" in the output.
+    * Technically, the sampleMetadata file in the output is derived from the negative ionization-mode sampleMetadata.