--- a/raceid_filtnormconf.xml	Thu Feb 28 17:40:54 2019 -0500
+++ b/raceid_filtnormconf.xml	Mon Apr 15 17:55:17 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.2" >
+<tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.3" >
     <description>generates a normalised and filtered count matrix of single-cell RNA data</description>
     <macros>
         <import>macros.xml</import>
@@ -7,13 +7,13 @@
     <expand macro="requirements" />
     <version_command><![CDATA[
 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
-]]></version_command>
+]]>
+    </version_command>
 
     <command detect_errors="exit_code"><![CDATA[
 #set bin = 'cluster.R'
 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null
     ]]></command>
-  
     <configfiles>
         <configfile name="userconf" ><![CDATA[
 @STRING2VECTOR@
@@ -28,6 +28,7 @@
             <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." />
             <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" />
             <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted"  />
+            <param name="hist_geq_one" type="boolean" checked="false" label="Count filtered features greater than or equal to 1" help="By default features are counted if they are above zero, but RaceID adds 0.1 to all counts after normalisation to create a non-zero dataset."  />
             <expand macro="use_defaults_no" >
                 <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" />
                 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
@@ -65,24 +66,22 @@
                         <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
                     </when>
                 </conditional>
-                <param name="use_log" type="boolean" checked="false" label="Output Log?" />
             </expand>
-        </section>                    
+        </section>
     </inputs>
     <outputs>
         <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
         <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
-        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
-            <filter>use_log</filter>
-        </data>
+        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics"  />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
             <param name="intable" value="use.intestinal" />
             <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
+            <output name="outlog" value="intestinal.filter.log" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- defaults, feeding in a matrix with reduced filtering -->
             <param name="intable" value="matrix.tabular" />
             <section name="filt" >
@@ -93,7 +92,7 @@
             <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" />
             <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
             <param name="intable" value="use.intestinal" />
             <section name="filt" >
@@ -108,7 +107,15 @@
             </section>
             <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
+            <!-- defaults, but histogram adjustment  -->
+            <param name="intable" value="use.intestinal" />
+            <section name="filt" >
+                <param name="hist_geq_one" value="true" />
+            </section>
+            <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
+        </test>
+        <test expect_num_outputs="3">
             <!-- Advanced. Opts, CC used  -->
             <param name="intable" value="use.intestinal" />
             <section name="filt" >
@@ -136,7 +143,7 @@
             <output name="outpdf" value="intestinal_advanced.filter.pdf" compare="sim_size" delta="150" />
         </test>
     </tests>
-        <help><![CDATA[
+    <help><![CDATA[
 RaceID3
 =======
 
@@ -171,6 +178,6 @@
 A PDF report will be generated giving metrics about the library size and number of features as histograms, and additional metrics relating to cell-cycle correction will be produced if that option has been selected.
 
 ]]>
-        </help>
-        <expand macro="citations" />
+    </help>
+    <expand macro="citations" />
 </tool>