--- a/parse.xml	Fri Jun 27 20:32:33 2025 +0000
+++ b/parse.xml	Fri Jul 25 13:54:01 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy2" profile="23.2" license="MIT">
     <description>Find ligation pairs in alignments and create pairs.</description>
     <macros>
         <import>macros.xml</import>
@@ -21,6 +21,9 @@
             #if $output_stats:
                 '$parsed_pairs_stats'
             #end if
+            #if $select_add_columns.add_columns_selection == "yes":
+                --add-columns '$select_add_columns.add_columns'
+            #end if
             --walks-policy '$walks_policy'
             --max-inter-align-gap '$max_inter_algn_gap'
             --nproc-in \${GALAXY_SLOTS:-4}
@@ -36,6 +39,31 @@
         <param argument="--drop-seq" type="boolean" truevalue="--drop-seq" falsevalue="" checked="False" label="remove sequences and PHREDs from the sam fields"></param>
         <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>
         <param argument="--drop-sam" type="boolean" truevalue="--drop-sam" falsevalue="" checked="False" label="Do not add sams to the output"></param>    
+        <conditional name="select_add_columns">
+            <param name="add_columns_selection" type="select" label="Add additional columns to the output" help="Select if additional columns needs to be added to the output pairs file.">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param argument="--add-columns" type="select" multiple="true" label="Select extra columns describing alignments" help="Multiple options can be selected.">
+                    <option value="mapq">MAPQ</option>
+                    <option value="pos5">POS5</option>
+                    <option value="pos3">POS3</option>
+                    <option value="cigar">CIGAR</option>
+                    <option value="read_len">Read length</option>
+                    <option value="matched_bp">Matched bp</option>
+                    <option value="algn_ref_span">algn_ref_span</option>
+                    <option value="dist_to_5">dist_to_5</option>
+                    <option value="dist_to_3">dist_to_3</option>
+                    <option value="seq">seq</option>
+                    <option value="mismatches">mismatches</option>
+                    <option value="read_side">read_side</option>
+                    <option value="algn_idx">algn_idx</option>
+                    <option value="same_side_algn_count">same_side_algn_count</option>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
         <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
             <expand macro="walks_policy_options"/>
         </param>   
@@ -43,7 +71,7 @@
     </inputs>
     <outputs>
         <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
-        <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
+        <data name="parsed_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: parsed.stats">
             <filter>output_stats</filter>
         </data>
     </outputs>
@@ -124,6 +152,19 @@
             <param name="max_inter_algn_gap" value="20"/>
             <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
         </test>
+        <!--Test 09 with SAM file as input and add columns-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="min_mapq" value="1"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <conditional name="select_add_columns">
+                <param name="add_columns_selection" value="yes"/>
+                <param name="add_columns" value="mapq,seq"/>
+            </conditional>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
+        </test>
 
     </tests>
     <help><![CDATA[