# HG changeset patch
# User eschen42
# Date 1569963478 14400
# Node ID 38f509903a0b6d3400977a5152443183cb1f144b
# Parent  9f5c0e23c2056310e1006b923f23ebecb93b94f1
"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"

diff -r 9f5c0e23c205 -r 38f509903a0b test-data/expected_dataMatrix.tsv
--- a/test-data/expected_dataMatrix.tsv	Mon Sep 03 22:34:35 2018 -0400
+++ b/test-data/expected_dataMatrix.tsv	Tue Oct 01 16:57:58 2019 -0400
@@ -3,7 +3,7 @@
 HMDB00208	747080	595872	3143654	4059767	1433702	5593888	2477288	3346077	4230072
 HMDB00251	368600	94936	293988	352855	767894	268331	310918	1248919	577184
 HMDB00299	250551	456162	808657	614370	250403	768004	504108	1014041	1362408
-HMDB00512	0	280560	556003	590779	209285	342532	569970	525240	246282
+HMDB00512	525240	280560	556003	590779	209285	342532	569970	525240	246282
 HMDB00518	0	85944	129886	175800	13154	230242	440223	315368	10657
 HMDB00715	1252089	905408	5140022	2658555	814523	2558923	4184204	3865723	3236644
 HMDB01032	2569205	1604999	26222916	257139	675754	59906109	31151730	18648127	14989438
diff -r 9f5c0e23c205 -r 38f509903a0b test-data/rangefilter_dataMatrix.tsv
--- a/test-data/rangefilter_dataMatrix.tsv	Mon Sep 03 22:34:35 2018 -0400
+++ b/test-data/rangefilter_dataMatrix.tsv	Tue Oct 01 16:57:58 2019 -0400
@@ -1,6 +1,6 @@
-	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_208
-HMDB00191	19.0950724540801	19.5573683394871	19.1351832076319	18.581538968171	19.7610090032025	19.5831195045026	19.3006944055142	19.1741869272827	19.8736633887651	19.7958256457729	19.2864427002132	20.0597101691826	20.4262862563728	21.1281900906526	20.2494039981067	20.8917666482316	19.438513703552	19.5608253922588	19.2486364146654
-HMDB00208	19.5109032146715	23.6779611010349	19.1846429313023	20.1610039089984	22.7740711828923	21.5840110083096	21.9529654992985	20.451313755289	22.4154199380002	22.3652301844309	21.2403301698498	21.6740392144135	22.0122507889717	22.8615935600174	23.0952006159265	23.3011358356974	22.746605551146	20.5866803867983	21.2764220576728
-HMDB01032	21.2928905785523	24.6332887213057	20.6141409677961	18.7154961966847	22.9501240553341	24.6443247870262	17.9721889132336	19.3661386209868	25.8361997953493	18.0050049466979	24.8928089492302	24.1525273990616	23.8374429574498	20.5681658146509	24.2713659930314	22.4140893053724	19.7323297568288	13.958552715431	15.4342372710269
-HMDB01101.1	22.7134708439962	15.6722319530667	11.6247954558602	23.3631578345615	17.8085620299575	22.183613575742	21.8871689158671	19.8971659609365	19.6661147561338	19.214418735272	20.6142092807528	16.1361300108053	18.7553505325418	20.079142288524	20.4818181509538	14.9315685693242	21.3775881248719	16.1536311941017	14.9054340159519
-HMDB13189	21.3346290086766	19.4727602406215	20.6639784491577	19.2400016764968	17.0561931543153	21.3938481405109	19.1797706242895	19.6763582845664	21.7496566885488	20.9339312108399	20.6175661105571	21.7167470481744	20.8887603396637	16.7978767996065	21.5788388647145	21.4643567902489	20.9969706149343	19.9807336965562	19.6828797432404
+	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_149	HU_152	HU_175	HU_178	HU_185	HU_208
+HMDB00191	19.0950724540801	19.5573683394871	19.1351832076319	18.581538968171	19.7610090032025	19.5831195045026	19.3006944055142	19.1741869272827	19.8736633887651	19.7958256457729	19.2864427002132	21.1281900906526	20.2494039981067	20.8917666482316	19.438513703552	19.5608253922588	19.2486364146654
+HMDB00208	19.5109032146715	23.6779611010349	19.1846429313023	20.1610039089984	22.7740711828923	21.5840110083096	21.9529654992985	20.451313755289	22.4154199380002	22.3652301844309	21.2403301698498	22.8615935600174	23.0952006159265	23.3011358356974	22.746605551146	20.5866803867983	21.2764220576728
+HMDB01032	21.2928905785523	24.6332887213057	20.6141409677961	18.7154961966847	22.9501240553341	24.6443247870262	17.9721889132336	19.3661386209868	25.8361997953493	18.0050049466979	24.8928089492302	20.5681658146509	24.2713659930314	22.4140893053724	19.7323297568288	13.958552715431	15.4342372710269
+HMDB01101.1	22.7134708439962	15.6722319530667	11.6247954558602	23.3631578345615	17.8085620299575	22.183613575742	21.8871689158671	19.8971659609365	19.6661147561338	19.214418735272	20.6142092807528	20.079142288524	20.4818181509538	14.9315685693242	21.3775881248719	16.1536311941017	14.9054340159519
+HMDB13189	21.3346290086766	19.4727602406215	20.6639784491577	19.2400016764968	17.0561931543153	21.3938481405109	19.1797706242895	19.6763582845664	21.7496566885488	20.9339312108399	20.6175661105571	16.7978767996065	21.5788388647145	21.4643567902489	20.9969706149343	19.9807336965562	19.6828797432404
diff -r 9f5c0e23c205 -r 38f509903a0b test-data/rangefilter_sampleMetadata.tsv
--- a/test-data/rangefilter_sampleMetadata.tsv	Mon Sep 03 22:34:35 2018 -0400
+++ b/test-data/rangefilter_sampleMetadata.tsv	Tue Oct 01 16:57:58 2019 -0400
@@ -10,8 +10,6 @@
 HU_099	46	pos	23	21.3	M
 HU_110	53	pos	50	20.9	F
 HU_130	63	pos	33	26.06	M
-HU_134	67	pos	48	22.89	M
-HU_138	68	pos	42	21.88	M
 HU_149	72	pos	35	19.49	F
 HU_152	75	pos	26	17.58	F
 HU_175	87	pos	35	21.26	F
diff -r 9f5c0e23c205 -r 38f509903a0b w4mclassfilter.xml
--- a/w4mclassfilter.xml	Mon Sep 03 22:34:35 2018 -0400
+++ b/w4mclassfilter.xml	Tue Oct 01 16:57:58 2019 -0400
@@ -1,27 +1,28 @@
-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.11">
+<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.13">
     <description>Filter W4m data by values or metadata</description>
     <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
     <requirements>
-        <!-- <requirement type="package" version="6.2">readline</requirement> -->
-        <requirement type="package" version="3.4.1">r-base</requirement>
-        <requirement type="package" version="1.1_4">r-batch</requirement>
-        <requirement type="package" version="0.98.8">w4mclassfilter</requirement>
+        <requirement type="package" version="3.6.1">r-base</requirement>
+        <requirement type="package" version="1.1_5">r-batch</requirement>
+        <requirement type="package" version="0.98.13">w4mclassfilter</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
+    unset R_HOME;
     Rscript $__tool_directory__/w4mclassfilter_wrapper.R
-    dataMatrix_in '$dataMatrix_in'
-    sampleMetadata_in '$sampleMetadata_in'
-    variableMetadata_in '$variableMetadata_in'
-    sampleclassNames '$sampleclassNames'
-    inclusive '$inclusive'
-    wildcards '$wildcards'
-    classnameColumn '$classnameColumn'
-    samplenameColumn 'sampleMetadata'
+    dataMatrix_in         '$dataMatrix_in'
+    sampleMetadata_in     '$sampleMetadata_in'
+    variableMetadata_in   '$variableMetadata_in'
+    sampleclassNames      '$sampleclassNames'
+    inclusive             '$inclusive'
+    wildcards             '$wildcards'
+    classnameColumn       '$classnameColumn'
+    samplenameColumn      'sampleMetadata'
     variable_range_filter '$variableRangeFilter'
-    transformation '$transformation'
-    dataMatrix_out '$dataMatrix_out'
-    sampleMetadata_out '$sampleMetadata_out'
-    variableMetadata_out '$variableMetadata_out'
+    transformation        '$transformation'
+    imputation            '$imputation'
+    dataMatrix_out        '$dataMatrix_out'
+    sampleMetadata_out    '$sampleMetadata_out'
+    variableMetadata_out  '$variableMetadata_out'
     ]]></command>
     <inputs>
         <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
@@ -95,6 +96,12 @@
             <option value="log2">log2</option>
             <option value="log10">log10</option>
         </param>
+        <param name="imputation" label="Imputation of missing values" type="select"
+            help="'zero' (the default) - replace missing values with zero; 'center' - replace missing values with feature-median; 'none' - perform no imputation">
+            <option value="zero" selected="true">zero</option>
+            <option value="center">center</option>
+            <option value="none">none</option>
+        </param>
     </inputs>
     <outputs>
         <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
@@ -110,16 +117,27 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="M"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
-        <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
-        <param name="transformation" value="log10"/>
+        <param name="inclusive" value="TRUE"/>
+        <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
+        <param name="transformation" value="none"/>
         <output name="dataMatrix_out">
           <assert_contents>
-            <has_text text="5.87336711011293" />
+            <has_text text="747080" />
+            <not_has_text text="13420742" />
+            <not_has_text text="47259" />
           </assert_contents>
         </output>
         <output name="sampleMetadata_out">
           <assert_contents>
+            <has_text text="HU_017" />
+            <has_text text="HU_034" />
+            <has_text text="HU_078" />
+            <has_text text="HU_091" />
+            <has_text text="HU_093" />
+            <has_text text="HU_099" />
+            <has_text text="HU_130" />
+            <has_text text="HU_134" />
+            <has_text text="HU_138" />
             <not_has_text text="HU_028" />
             <not_has_text text="HU_051" />
             <not_has_text text="HU_060" />
@@ -131,94 +149,87 @@
             <not_has_text text="HU_185" />
             <not_has_text text="HU_204" />
             <not_has_text text="HU_208" />
-            <has_text text="HU_017" />
-            <has_text text="HU_034" />
-            <has_text text="HU_078" />
-            <has_text text="HU_091" />
-            <has_text text="HU_093" />
-            <has_text text="HU_099" />
-            <has_text text="HU_130" />
-            <has_text text="HU_134" />
-            <has_text text="HU_138" />
           </assert_contents>
         </output>
         <output name="variableMetadata_out">
           <assert_contents>
+            <has_text     text="HMDB00208" />
+            <has_text     text="HMDB01032" />
+            <has_text     text="HMDB01101.1" />
+            <has_text     text="HMDB13189" />
             <not_has_text text="HMDB00191" />
-            <has_text     text="HMDB00208" />
             <not_has_text text="HMDB00251" />
             <not_has_text text="HMDB00299" />
             <not_has_text text="HMDB00512" />
             <not_has_text text="HMDB00518" />
             <not_has_text text="HMDB00715" />
             <not_has_text text="HMDB00822" />
-            <has_text     text="HMDB01032" />
-            <has_text     text="HMDB01101.1" />
             <not_has_text text="HMDB03193" />
             <not_has_text text="HMDB04824" />
             <not_has_text text="HMDB10348" />
-            <has_text     text="HMDB13189" />
             <not_has_text text="HMDB59717" />
           </assert_contents>
         </output>
       </test>
       <!-- test 2 -->
-      <test>
+	  <test>
         <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
         <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
         <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
-        <param name="classnameColumn" value="sampleMetadata"/>
         <!-- test that hyphens in regular expressions work -->
         <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
+        <param name="inclusive" value="TRUE"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
-        <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/>
-        <param name="transformation" value="log2"/>
-        <output name="dataMatrix_out">
+        <param name="classnameColumn" value="sampleMetadata"/>
+		<!-- test that variableRangeFilter works with tranformation -->
+		<param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
+        <param name="transformation" value="log10"/>
+        <param name="imputation" value="zero"/>
+        <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
           <assert_contents>
-            <has_text text="19.5109032146715" />
+			<has_text text="5.8733671" />
           </assert_contents>
         </output>
         <output name="sampleMetadata_out">
           <assert_contents>
+            <has_text text="HU_017" />
             <has_text text="HU_028" />
+            <has_text text="HU_034" />
             <has_text text="HU_051" />
             <has_text text="HU_060" />
+            <has_text text="HU_078" />
+            <has_text text="HU_091" />
+            <has_text text="HU_093" />
+            <has_text text="HU_099" />
             <has_text text="HU_110" />
+            <has_text text="HU_130" />
+            <has_text text="HU_134" />
+            <has_text text="HU_138" />
             <has_text text="HU_149" />
             <has_text text="HU_152" />
             <has_text text="HU_175" />
             <has_text text="HU_178" />
             <has_text text="HU_185" />
+            <has_text text="HU_208" />
             <not_has_text text="HU_204" />
-            <has_text text="HU_208" />
-            <has_text text="HU_017" />
-            <has_text text="HU_034" />
-            <has_text text="HU_078" />
-            <has_text text="HU_091" />
-            <has_text text="HU_093" />
-            <has_text text="HU_099" />
-            <has_text text="HU_130" />
-            <has_text text="HU_134" />
-            <has_text text="HU_138" />
           </assert_contents>
         </output>
         <output name="variableMetadata_out">
           <assert_contents>
             <has_text     text="HMDB00191" />
             <has_text     text="HMDB00208" />
+            <has_text     text="HMDB01032" />
+            <has_text     text="HMDB01101.1" />
+            <has_text     text="HMDB13189" />
             <not_has_text text="HMDB00251" />
             <not_has_text text="HMDB00299" />
             <not_has_text text="HMDB00512" />
             <not_has_text text="HMDB00518" />
             <not_has_text text="HMDB00715" />
             <not_has_text text="HMDB00822" />
-            <has_text     text="HMDB01032" />
-            <has_text     text="HMDB01101.1" />
             <not_has_text text="HMDB03193" />
             <not_has_text text="HMDB04824" />
             <not_has_text text="HMDB10348" />
-            <has_text     text="HMDB13189" />
             <not_has_text text="HMDB59717" />
           </assert_contents>
         </output>
@@ -230,7 +241,7 @@
         <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="M"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <param name="transformation" value="none"/>
         <output name="dataMatrix_out">
           <assert_contents>
@@ -281,7 +292,13 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="*"/>
         <param name="wildcards" value="TRUE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
+        <param name="imputation" value="zero"/>
+        <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
+          <assert_contents>
+            <not_has_text text="NA" />
+          </assert_contents>
+        </output>
         <output name="sampleMetadata_out">
           <assert_contents>
             <not_has_text text="HU_204" />
@@ -315,7 +332,7 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="M"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <output name="sampleMetadata_out">
           <assert_contents>
             <not_has_text text="HU_028" />
@@ -349,7 +366,7 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="M"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <output name="variableMetadata_out">
           <assert_contents>
             <has_text     text="HMDB03193" />
@@ -379,7 +396,7 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="M"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <output name="variableMetadata_out">
           <assert_contents>
             <has_text     text="HMDB03193" />
@@ -409,7 +426,7 @@
         <param name="classnameColumn" value="gender"/>
         <param name="sampleclassNames" value="[Mm],[fF]"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <output name="sampleMetadata_out">
           <assert_contents>
             <has_text text="HU_028" />
@@ -443,7 +460,7 @@
         <param name="classnameColumn" value=""/>
         <param name="sampleclassNames" value="M"/>
         <param name="wildcards" value="FALSE"/>
-        <param name="inclusive" value="filter-in"/>
+        <param name="inclusive" value="TRUE"/>
         <output name="sampleMetadata_out">
           <assert_contents>
             <has_text text="HU_028" />
@@ -469,6 +486,54 @@
           </assert_contents>
         </output>
       </test>
+      <!-- test 10 - extends test4 with no imputation rather than zero imputation -->
+      <test>
+        <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
+        <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
+        <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
+        <param name="classnameColumn" value="gender"/>
+        <param name="sampleclassNames" value="*"/>
+        <param name="wildcards" value="TRUE"/>
+        <param name="inclusive" value="TRUE"/>
+        <param name="imputation" value="none"/>
+        <output name="dataMatrix_out" md5="cc9ab8bdb70b68b43b19b7327d285166">
+          <assert_contents>
+            <not_has_text text="HU_204" />
+            <has_text text="NA" />
+            <has_text text="HU_028" />
+          </assert_contents>
+        </output>
+        <output name="sampleMetadata_out">
+          <assert_contents>
+            <not_has_text text="HU_204" />
+            <has_text text="HU_028" />
+          </assert_contents>
+        </output>
+      </test>
+      <!-- test 11 - extends test4 with center imputation rather than zero imputation -->
+      <test>
+        <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
+        <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
+        <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
+        <param name="classnameColumn" value="gender"/>
+        <param name="sampleclassNames" value="*"/>
+        <param name="wildcards" value="TRUE"/>
+        <param name="inclusive" value="TRUE"/>
+        <param name="imputation" value="center"/>
+        <output name="dataMatrix_out" md5="75a4802bb8887709e4d4dec8c2c3d3cf">
+          <assert_contents>
+            <not_has_text text="HU_204" />
+            <not_has_text text="NA" />
+            <has_text text="HU_028" />
+          </assert_contents>
+        </output>
+        <output name="sampleMetadata_out">
+          <assert_contents>
+            <not_has_text text="HU_204" />
+            <has_text text="HU_028" />
+          </assert_contents>
+        </output>
+      </test>
     </tests>
     <help><![CDATA[
 
@@ -531,13 +596,13 @@
 
 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
 
-- Missing values in dataMatrix are imputed to zero.
-- The values in the dataMatrix may be log-transformed if desired.
 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
 - Features and samples that have zero variance are eliminated.
 - Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.
 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
+- If desired, the values in the dataMatrix may be log-transformed.
+- If desired, each missing value in dataMatrix is replaced with zero or the median value observed for the corresponding feature.
 
 This tool may be applied several times sequentially, which may be useful for:
 
@@ -607,10 +672,15 @@
 	|
 
 Data-transformation (default = '``none``')
-	| '``none``' - do not transform data matrix values
-	| '``log2``' - take the log base 2 of the values in the data matrix
-	| '``log10``' - take the log base 10 of the values in the data matrix
-	| In both cases, negative and missing values are imputed to zero.
+	| '``none``' - Do not transform data matrix values.
+	| '``log2``' - Take the log base 2 of the values in the data matrix.
+	| '``log10``' - Take the log base 10 of the values in the data matrix.
+	|
+
+Data-imputation (default = '``zero``')
+	| '``none``' - Do not impute data matrix values.
+	| '``zero``' - Negative and missing values are imputed to zero.
+	| '``center``' - For each feature, negative and missing values are imputed to the median of other values.
 	|
 
 
@@ -708,14 +778,22 @@
 
   - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
 
+----------------------------------
+Data transformation and imputation
+----------------------------------
+
+Data may optionally be log2- or log10-transformed.
+
+Negative intensity values are always substituted with zeros.
+
+Missing intensity data values may optionally be imputed.  Missing values may be substituted with zeros (as may be appropriate for univariate analysis) or with the median for the feature (as may be appropriate for multivariate analysis).  (Note that the median feature-intensity is computed for the samples *before* variable-range filters are applied.)
+
 -----------------------------------------------------------------------------
 
 ----------------
 WORKING EXAMPLES
 ----------------
 
-.. class:: infomark
-
 -----------
 Input Files
 -----------
@@ -730,8 +808,6 @@
 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv          |
 +------------------------------------------------------------------------------------------------------------------------------------------------------+
 
-.. class:: infomark
-
 -------------------------------
 Running Without Range-Filtering
 -------------------------------
@@ -740,19 +816,23 @@
 
 **Input parameters**
 
-+------------------------------------+-------------------------------+
-| Input Parameter                    | Value                         |
-+====================================+===============================+
-| Names of sample-classes            | M                             |
-+------------------------------------+-------------------------------+
-| Include named classes              | filter-in                     |
-+------------------------------------+-------------------------------+
-| Column that names the sample-class | gender                        |
-+------------------------------------+-------------------------------+
-| Variable range-filters             | (Leave this field empty.)     |
-+------------------------------------+-------------------------------+
-| Data transforamtion                | none                          |
-+------------------------------------+-------------------------------+
++---------------------------------------------+-------------------------------+
+| Input Parameter                             | Value                         |
++=============================================+===============================+
+| Column that names the sample-class          | gender                        |
++---------------------------------------------+-------------------------------+
+| Names of sample-classes                     | M                             |
++---------------------------------------------+-------------------------------+
+| Use 'wild-cards' or 'regular expressions'   | wild-cards                    |
++---------------------------------------------+-------------------------------+
+| Exclude/include named classes               | filter-in                     |
++---------------------------------------------+-------------------------------+
+| Variable range-filters                      | (Leave this field empty.)     |
++---------------------------------------------+-------------------------------+
+| Data transforamtion                         | none                          |
++---------------------------------------------+-------------------------------+
+| Missing-value imputation                    | center                        |
++---------------------------------------------+-------------------------------+
 
 **Expected outputs**
 
@@ -766,8 +846,6 @@
 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv  |
 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
 
-.. class:: infomark
-
 ----------------------------
 Running With Range-Filtering
 ----------------------------
@@ -777,19 +855,23 @@
 
 **Input parameters**
 
-+------------------------------------+------------------------------------+
-| Input Parameter                    | Value                              |
-+====================================+====================================+
-| Names of sample-classes            | (Leave this field empty.)          |
-+------------------------------------+------------------------------------+
-| Include named classes              | filter-out                         |
-+------------------------------------+------------------------------------+
-| Column that names the sample-class | gender                             |
-+------------------------------------+------------------------------------+
-| Variable range-filters             | FEATMAX:20.93157:,mz:200:,rt::800  |
-+------------------------------------+------------------------------------+
-| Data transforamtion                | log2                               |
-+------------------------------------+------------------------------------+
++---------------------------------------------+-----------------------------------+
+| Input Parameter                             | Value                             |
++=============================================+===================================+
+| Column that names the sample-class          | sampleMetadata                    |
++---------------------------------------------+-----------------------------------+
+| Names of sample-classes                     | HU_13[48]                         |
++---------------------------------------------+-----------------------------------+
+| Use 'wild-cards' or 'regular expressions'   | regular-expressions               |
++---------------------------------------------+-----------------------------------+
+| Exclude/include named classes               | filter-out                        |
++---------------------------------------------+-----------------------------------+
+| Variable range-filters                      | FEATMAX:20.93157:,mz:200:,rt::800 |
++---------------------------------------------+-----------------------------------+
+| Data transforamtion                         | log2                              |
++---------------------------------------------+-----------------------------------+
+| Missing-value imputation                    | zero                              |
++---------------------------------------------+-----------------------------------+
 
 **Expected outputs**
 
diff -r 9f5c0e23c205 -r 38f509903a0b w4mclassfilter_wrapper.R
--- a/w4mclassfilter_wrapper.R	Mon Sep 03 22:34:35 2018 -0400
+++ b/w4mclassfilter_wrapper.R	Tue Oct 01 16:57:58 2019 -0400
@@ -23,8 +23,8 @@
 
 suppressMessages(library(w4mclassfilter))
 
-if(packageVersion("w4mclassfilter") < "0.98.0")
-    stop("Please use 'w4mclassfilter' versions of 0.98.0 and above")
+if(packageVersion("w4mclassfilter") < "0.98.12")
+    stop("Please use 'w4mclassfilter' versions of 0.98.12 and above")
 
 ## constants
 ##----------
@@ -83,6 +83,16 @@
 # other parameters
 
 transformation <- as.character(argVc["transformation"])
+my_imputation_label <- as.character(argVc["imputation"])
+my_imputation_function <- if (my_imputation_label == "zero") {
+  w4m_filter_zero_imputation
+} else if (my_imputation_label == "center") {
+  w4m_filter_median_imputation
+} else if (my_imputation_label == "none") {
+  w4m_filter_no_imputation
+} else {
+  stop(sprintf("Unknown value %s supplied for 'imputation' parameter.  Expected one of {zero,center,none}."))
+}
 wildcards <- as.logical(argVc["wildcards"])
 sampleclassNames <- as.character(argVc["sampleclassNames"])
 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
@@ -100,37 +110,39 @@
 ## -----------------------------
 ## Transformation and imputation
 ## -----------------------------
-my_w4m_filter_imputation <- if (transformation == "log10") {
+my_transformation_and_imputation <- if (transformation == "log10") {
   function(m) {
     if (!is.matrix(m))
-      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+      stop("Cannot transform and impute data - the supplied data is not in matrix form")
     if (nrow(m) == 0)
-      stop("Cannot impute and transform data - data matrix has no rows")
+      stop("Cannot transform and impute data - data matrix has no rows")
     if (ncol(m) == 0)
-      stop("Cannot impute and transform data - data matrix has no columns")
-    suppressWarnings(
+      stop("Cannot transform and impute data - data matrix has no columns")
+    suppressWarnings({
       # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
       m <- log10(m)
-    )
-    return ( w4m_filter_imputation(m) )
+      m[is.na(m)] <- NA
+    })
+    return ( my_imputation_function(m) )
   }
 } else if (transformation == "log2") {
   function(m) {
     if (!is.matrix(m))
-      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+      stop("Cannot transform and impute data - the supplied data is not in matrix form")
     if (nrow(m) == 0)
-      stop("Cannot impute and transform data - data matrix has no rows")
+      stop("Cannot transform and impute data - data matrix has no rows")
     if (ncol(m) == 0)
-      stop("Cannot impute and transform data - data matrix has no columns")
-    suppressWarnings(
+      stop("Cannot transform and impute data - data matrix has no columns")
+    suppressWarnings({
       # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
       m <- log2(m)
-    )
-    return ( w4m_filter_imputation(m) )
+      m[is.na(m)] <- NA
+    })
+    return ( my_imputation_function(m) )
   }
 } else {
   # use the method from the w4mclassfilter class
-  w4m_filter_imputation
+  my_imputation_function
 }
 
 ##------------------------------
@@ -150,7 +162,7 @@
 , samplename_column     = samplenameColumn
 , variable_range_filter = variable_range_filter
 , failure_action        = my_print
-, data_imputation       = my_w4m_filter_imputation
+, data_imputation       = my_transformation_and_imputation
 )
 
 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",