--- a/dropletutils.xml	Wed Jan 29 20:07:15 2020 +0000
+++ b/dropletutils.xml	Thu Dec 10 13:49:40 2020 +0000
@@ -1,9 +1,22 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
+<tool id="dropletutils" name="DropletUtils" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
     <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
+    <xrefs>
+        <xref type="bio.tools">dropletutils</xref>
+    </xrefs>
+    <edam_topics>
+        <edam_topic>topic_0203</edam_topic>
+        <edam_topic>topic_3168</edam_topic>
+        <edam_topic>topic_3170</edam_topic>
+        <edam_topic>topic_3308</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_1812</edam_operation>
+        <edam_operation>operation_3200</edam_operation>
+    </edam_operations>
     <macros>
-        <token name="@PACKAGE_VERSION@" >1.2.1</token>
-        <token name="@GALAXY_VERSION@" >galaxy6</token>
+        <token name="@TOOL_VERSION@">1.10.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@TXIN@">tenx.input</token>
         <token name="@TXOUT@">tenx.output</token>
         <xml name="test_dirin" >
@@ -16,9 +29,10 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement>
-        <requirement type="package" version="1.2_17" >r-matrix</requirement>
-        <requirement type="package" version="1.10.1" >bioconductor-scater</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-dropletutils</requirement>
+        <requirement type="package" version="1.18.0" >bioconductor-scater</requirement>
+        <requirement type="package" version="4.0">r-base</requirement>
+        <requirement type="package" version="1.2_18">r-matrix</requirement>
         <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
     </requirements>
     <version_command><![CDATA[
@@ -45,14 +59,14 @@
     <configfiles>
         <configfile name="droplet_conf" >
 ## defaults
-empty.fdr_threshold = 0.01
-eparams=formals(emptyDrops)
-dparams=formals(defaultDrops)
-bparams=formals(barcodeRanks)
+empty_fdr_threshold = 0.01
+eparams = formals(emptyDrops)
+dparams = formals(defaultDrops)
+bparams = formals(barcodeRanks)
 
 ## File params
-in.type='$tenx_format.use'
-out.type=NULL
+intype='$tenx_format.use'
+outtype=NULL
 
 files=list()
 files\$table='$table'
@@ -74,10 +88,10 @@
     #else if str($operation.method.use) == 'emptydrops':
 do.method="emptyDrops"
 eparams\$lower=as.integer('$operation.method.lower')
-empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh')
+empty_fdr_threshold=as.numeric('$operation.method.fdr_thresh')
     #end if
 
-out.type='$operation.outformat'
+outtype='$operation.outformat'
     #if str($operation.outformat) == 'directory':
 files\$out='@TXOUT@'
     #else if str($operation.outformat) == 'h5':
@@ -172,8 +186,8 @@
     </outputs>
     <tests>
         <!-- Directory input tests -->
-        <!-- ::: Default Drops -->
         <test expect_num_outputs="1">
+            <!-- ::: Default Drops -->
             <expand macro="test_dirin" />
             <conditional name="operation">
                 <param name="use" value="filter" />
@@ -196,17 +210,17 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- :: Barcode Ranks -->
         <test expect_num_outputs="1">
+            <!-- :: Barcode Ranks -->
             <expand macro="test_dirin" />
             <conditional name="operation">
                 <param name="use" value="barcode_rank" />
                 <param name="lower" value="120" />
             </conditional>
-            <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/>
+            <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="600"/>
         </test>
-        <!-- ::: Empty Drops -->
         <test expect_num_outputs="3">
+            <!-- ::: Empty Drops -->
             <expand macro="test_dirin" />
             <conditional name="operation">
                 <param name="use" value="filter" />
@@ -221,16 +235,16 @@
             <output name="table" >
                 <assert_contents>
                     <has_n_columns n="9" />
-                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
-                    <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
-                    <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
+                    <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" />
+                    <has_line_matching expression="^994\sGGCATTACAA\s338\s-246\.(.*TRUE){3}$" />
+                    <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166\.(.*TRUE){3}$" />
                 </assert_contents>
             </output>
             <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
         </test>
         <!-- Other format input tests -->
-        <!-- ::: Empty Drops, same as above but input is h5 -->
         <test expect_num_outputs="3">
+            <!-- ::: Empty Drops, same as above but input is h5 -->
             <conditional name="tenx_format" >
                 <param name="use" value="h5" />
                 <param name="input" value="in_matrix.h5" />
@@ -248,9 +262,9 @@
             <output name="table" >
                 <assert_contents>
                     <has_n_columns n="9" />
-                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
-                    <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
-                    <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
+                    <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" />
+                    <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198\.(.*TRUE){3}$" />
+                    <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196\.(.*TRUE){3}$" />
                 </assert_contents>
             </output>
             <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />