Update RIAssigner from 0.4.1 to 0.6.1 with new click CLI

Co-authored-by: hechth <12066490+hechth@users.noreply.github.com>

Author: Copilot

tools/riassigner/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.4.1</token>
+    <token name="@TOOL_VERSION@">0.6.1</token>
     <xml name="creator">
         <creator>
             <person

tools/riassigner/riassigner.xml

@@ -1,4 +1,4 @@
-<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>compute retention indices</description>
     <macros>
         <import>macros.xml</import>
@@ -14,7 +14,7 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${output.ext}" &&
+        riassigner compute --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${output.ext}" &&
         cp -r 'output.${output.ext}' '${output}'
         ]]>
     </command>

tools/riassigner/riassigner_from_comment.xml

@@ -14,32 +14,11 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        python ${script} &&
-        #if $input.ext == "csv"
-        mv results.tsv ${output}
-        #else:
-        mv results.${input.ext} ${output}
-        #end if
+        riassigner ri-from-comment --query "$input" "$input.ext" "seconds" --ri-source "$format" --output "output.${output.ext}" &&
+        cp -r 'output.${output.ext}' '${output}'
         ]]>
     </command>
 
-    <configfiles>
-        <configfile name="script">
-from RIAssigner.data import PandasData, MatchMSData
-#if $input.ext in ["csv", "tsv", "parquet"]
-query = PandasData('${input}', '${input.ext}', rt_unit="seconds")
-#else
-query = MatchMSData('${input}', '${input.ext}', rt_unit="seconds")
-#end if
-query.init_ri_from_comment('${format}')
-#if $input.ext == "csv"
-query.write('results.tsv')
-#else
-query.write('results.${input.ext}')
-#end if
-        </configfile>
-    </configfiles>
-
     <inputs>
         <param name="input" type="data" format="csv,tsv,parquet,msp,mgf" label="Input File">
             <help>