# HG changeset patch
# User iuc
# Date 1637223993 0
# Node ID 953b4821b1837402e09f3dbbfee7c26670169eaa
# Parent  81bebc3027fc87e9469e723a7e91e44be966cd26
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 31bad8c5bf75981eafcd19ec6b00593f184fdeb8"

diff -r 81bebc3027fc -r 953b4821b183 macros.xml
--- a/macros.xml	Sat Oct 23 20:36:16 2021 +0000
+++ b/macros.xml	Thu Nov 18 08:26:33 2021 +0000
@@ -4,7 +4,7 @@
     <!-- macros applying to all umi_tools -->
 
     <token name="@TOOL_VERSION@">1.1.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="requirements">
         <requirements>
@@ -56,6 +56,8 @@
                 <add value="&#123;"/><!-- left brace -->
                 <add value="&#125;"/><!-- right brace -->
                 <add value="&#94;"/> <!-- caret -->
+                <add value="&#36;"/> <!-- dollar sign-->
+                <add value="&#43;" /><!-- plus sign -->
                 <add value="-"/>
                 <add value="!"/>
             </valid>
@@ -174,8 +176,8 @@
         <conditional name="extract_method_cond">
             <param argument="--extract-method" type="select" label="Barcode Extraction Method"
                    help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
-                <option value="string" selected="true" />
-                <option value="regex" />
+                <option value="string" selected="true">String</option>
+                <option value="regex">Regex</option>
             </param>
             <when value="string">
                 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
diff -r 81bebc3027fc -r 953b4821b183 umi-tools_whitelist.xml
--- a/umi-tools_whitelist.xml	Sat Oct 23 20:36:16 2021 +0000
+++ b/umi-tools_whitelist.xml	Thu Nov 18 08:26:33 2021 +0000
@@ -67,19 +67,19 @@
 
         <param argument="--method" type="select" label="Count reads or UMIs"
                help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent" >
-            <option value="reads" selected="true" />
-            <option value="umis" />
+            <option value="reads" selected="true">Reads</option>
+            <option value="umis">UMIs</option>
         </param>
         <!-- TODO Cannot use expect-cells with 'distance' knee method.-->
         <param argument="--knee-method" type="select" label="Method for detection of knee">
-            <option value="distance" selected="true" />
-            <option value="density"/>
+            <option value="distance" selected="true">Distance</option>
+            <option value="density">Density</option>
         </param>
         <param argument="--subset-reads" type="integer" min="0" value="0" label="Use the first N reads to automatically identify the true cell barcodes" />
         <param argument="--allow-threshold-error" type="boolean" truevalue="--allow-threshold-error" falsevalue="" label="Don't select a threshold" help="Will still output the plots if requested"/> 
         <param argument="--ed-above-threshold" type="select" optional="true" label="Detect and correct CBs above the threshold" help="which may be sequence errors from another CB">
-            <option value="correct">correct</option>
-            <option value="discard">discard</option>
+            <option value="correct">Correct</option>
+            <option value="discard">Discard</option>
         </param>
         <conditional name="celloptions" >
             <param name="use_cell_opts" type="select" label="Cell parameters" >