--- a/w4mcorcov.xml	Wed Sep 05 22:31:21 2018 -0400
+++ b/w4mcorcov.xml	Thu Nov 08 23:06:09 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.15">
+<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.16">
     <description>OPLS-DA Contrasts of Univariate Results</description>
     <macros>
         <xml name="paramPairSigFeatOnly">
@@ -201,13 +201,13 @@
           <has_text text="level1Level2Sig" />
           <!-- first matched line -->
           <has_text text="M349.2383T700" />
-          <has_text text="-0.3704185" />
+          <has_text text="-0.462909875" />
           <has_text text="-36.6668927" />
           <has_text text="0.4914638" />
           <has_text text="0.01302117" />
           <!-- second matched line -->
           <has_text text="M207.9308T206" />
-          <has_text text="0.3235022" />
+          <has_text text="0.504885262" />
           <has_text text="5.97529097" />
           <has_text text="0.207196379" />
           <has_text text="0.04438632" />
@@ -259,7 +259,7 @@
           <has_text text="level1Level2Sig" />
           <!-- first matched line -->
           <has_text text="M200.005T296" />
-          <has_text text="-0.24533821" />
+          <has_text text="-0.28035717" />
           <has_text text="-3.3573953" />
           <has_text text="0.1157346" />
           <has_text text="0.0647860" />
@@ -309,13 +309,13 @@
           <has_text text="vip4o" />
           <!-- first matched line -->
           <has_text text="M349.2383T700" />
-          <has_text text="-0.37867079" />
+          <has_text text="-0.4732226665" />
           <has_text text="-37.71066" />
           <has_text text="0.5246766" />
           <has_text text="0.0103341" />
           <!-- second matched line -->
           <has_text text="M207.9308T206" />
-          <has_text text="0.31570433" />
+          <has_text text="0.4927151212" />
           <has_text text="5.86655640" />
           <has_text text="0.2111623" />
           <has_text text="0.0488654" />
@@ -368,7 +368,7 @@
           <has_text text="NM516T251" />
           <has_text text="flower_yes" />
           <has_text text="other" />
-          <has_text text="0.03402807" />
+          <has_text text="0.3499550705" />
           <has_text text="0.03526926" />
           <has_text text="0.43664386" />
           <has_text text="0.587701897" />
@@ -419,13 +419,13 @@
           <has_text text="vip4o" />
           <!-- first matched line -->
           <has_text text="M349.2383T700" />
-          <has_text text="0.43361563" />
+          <has_text text="0.61594030" />
           <has_text text="37.76875778" />
           <has_text text="0.54672558" />
           <has_text text="0.3920409" />
           <!-- second matched line -->
           <has_text text="M207.9308T206" />
-          <has_text text="-0.3365475" />
+          <has_text text="-0.89716403" />
           <has_text text="-6.337903" />
           <has_text text="0.270297" />
           <has_text text="0.037661" />
@@ -454,14 +454,14 @@
           <has_text text="vip4o" />
           <!-- first matched line -->
           <has_text text="M349.2383T700" />
-          <has_text text="-0.0435663" />
-          <has_text text="-1.9068114" />
-          <has_text text="0.0304592" />
-          <has_text text="0.104748883" />
+          <has_text text="-0.331230562" />
+          <has_text text="-2.47167915" />
+          <has_text text="0.0892595" />
+          <has_text text="0.0049228872" />
         </assert_contents>
       </output>
     </test>
-    <!-- test #6 - issue 8 -->
+    <!-- test #7 - issue 8 -->
     <test>
       <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
       <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/>
@@ -495,6 +495,7 @@
 
 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
 
+**Release Notes** - https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper#release-notes
 
 Motivation
 ----------
@@ -616,9 +617,13 @@
   |
 
 [OUT] Contrast-detail output PDF
-  | Several plots for each two-projection OPLS-DA analysis:
+  | File containing several plots for each two-projection OPLS-DA analysis.
+
+- (first row, left) **correlation-versus-covariance plot** of OPLS-DA results
 
-- (first row, left) **correlation-versus-covariance plot** of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, *op. cit.*); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012), for use to identify features for consideration as biomarkers.
+    - This is a work-alike for the S-PLOT, computed using formula in equations 1 and 2 from Wiklund, (*op. cit.*);
+    - point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) increases through the range from 0.83 and 1.21 (Mehmood *et al.* 2012), for use to identify features for consideration as biomarkers;
+    - plot symbols are diamonds when the adjusted p-value of correlation is greater than 0.05, circles when it is less than 0.01, and triangles when it between these limits.
 - (second row, left) **model-overview plot** for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Th]]>&#233;<![CDATA[venot, 2017)
 - (first row, right) OPLS-DA **scores-plot** for the two projections (Th]]>&#233;<![CDATA[venot *et al.*, 2015)
 - (second row, right) **correlation-versus-covariance plot** of OPLS-DA results **orthogonal to the predictor** (see section "S-Plot of Orthogonal Component" in Wiklund, *op. cit.*, pp. 120-121; this characterizes features with the greatest variation independent of the predictor).
@@ -633,12 +638,18 @@
 - **featureID** - feature-identifier
 - **factorLevel1** - factor-level 1
 - **factorLevel2** - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels)
-- **correlation** - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in Supplement to Wiklund, *op. cit.*).  Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'.
-- **covariance** - covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in *ibid.*)
+- **correlation** - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from equation 2 in Wiklund, *op. cit.*).  Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'.
+- **covariance** - relative covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in *ibid.*, but scaled so that the greatest value has a magnitude of 1)
 - **vip4p** - "variable importance in projection" to the predictive projection, VIP\ :subscript:`4,p` (Galindo-Prieto *op. cit.*)
 - **vip4o** - "variable importance in projection" to the orthogonal projection, VIP\ :subscript:`4,o` (*ibid.*)
 - **loadp** - variable loading for the predictive projection (Wiklund *op. cit.*)
 - **loado** - variable loading for the orthogonal projection (*ibid.*)
+- **cor_p_val_raw** - p-value for Fisher-transformed correlation (Fisher, 1921; Snedecor, 1980; see also https://en.wikipedia.org/wiki/Fisher_transformation), with no family-wise error-rate correction.
+- **cor_p_value** - p-value for Fisher-transformed correlation, adjusted for family-wise error rate (Yekutieli *et al.*, 2001).  Caveat: any previous selection for features that vary notably by factor level may result in too little adjustment.
+- **cor_ci_lower** - lower limit of 95% confidence interval for correlation (see e.g. https://en.wikipedia.org/wiki/Fisher_transformation)
+- **cor_ci_upper** - upper limit of 95% confidence interval for correlation (*ibid.*)
+- **mz** - *m/z* ratio for feature, copied from input variableMetadata
+- **rt** - retention time for feature, copied from input variableMetadata
 - **level1Level2Sig** - (Only present when a test other than "none" is chosen) '1' when feature varies significantly across all classes (i.e., not pair-wise); '0' otherwise
 
 [OUT] Feature "Salience" data TABULAR
@@ -819,6 +830,19 @@
   <citations>
     <!-- this tool -->
     <citation type="doi">10.5281/zenodo.1034784</citation>
+    <!-- Fisher_1921: Fisher z-transformation of correlation coefficient -->
+    <citation type="bibtex"><![CDATA[
+    @article{Fisher_1921,
+      author = {Fisher, R. A.},
+      title = {{On the probable error of a coefficient of correlation deduced from a small sample}},
+      journal = {Metron},
+      year = {1921},
+      volume = {1},
+      pages = {3--32},
+      note = {Defines the Fisher z-transformation of a coefficient of correlation.  Citation adapted from http://www.citeulike.org/group/894/article/2344770},
+      url = {https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15169/1/14.pdf},
+    }
+    ]]></citation>
     <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->
     <citation type="doi">10.1002/cem.2627</citation>
     <!-- Giacomoni_2014 W4M 2.5 -->
@@ -833,6 +857,22 @@
     <citation type="doi">10.3389/fmolb.2016.00026</citation>
     <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
     <citation type="doi">10.1038/srep22274</citation>
+    <!-- Snedecor_1980: Fisher z-transformation of correlation coefficient -->
+    <citation type="bibtex"><![CDATA[
+    @book{Snedecor_1980,
+      author = {Snedecor, George W. and Cochran, William G.},
+      title = {Statistical methods},
+      publisher = {Iowa State University Press},
+      year = {1980},
+      pages = {186},
+      isbn = {0813815606},
+      language = {eng},
+      keyword = {Statistics, Statistics as Topic -- methods},
+      lccn = {80014582},
+      edition = {7th ed..},
+      address = {Ames, Iowa},
+    }
+    ]]></citation>
     <!-- Thevenot_2015 Urinary metabolome statistics -->
     <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
     <!-- ropls package -->
@@ -849,6 +889,8 @@
     ]]></citation>
     <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
     <citation type="doi">10.1021/ac0713510</citation>
+    <!-- Yekutieli_2001 The control of the false discovery rate in multiple testing under dependency -->
+    <citation type="doi">10.1214/aos/1013699998</citation>
   </citations>
   <!--
      vim:et:sw=4:ts=4