# HG changeset patch
# User iuc
# Date 1712161530 0
# Node ID 8fae6be7a507a53b41278e34aa8c2bbf3bf3d344
# Parent  68413c5eb03596d9fc7d0df5d58ec51aac4a91a2
planemo upload for repository https://github.com/open2c/pairtools commit 17acbcae8309bec856882bc4aef1899d613f6807

diff -r 68413c5eb035 -r 8fae6be7a507 parse.xml
--- a/parse.xml	Tue Mar 26 12:49:21 2024 +0000
+++ b/parse.xml	Wed Apr 03 16:25:30 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05" license="MIT">
+<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
     <description>Find ligation pairs in alignments and create pairs.</description>
     <macros>
         <import>macros.xml</import>
@@ -40,7 +40,7 @@
         <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
     </inputs>
     <outputs>
-        <data name="output_parsed_pairs" format="pairs" label="${tool.name} on ${on_string}: .pairs"/>
+        <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
         <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
             <filter>output_stats</filter>
         </data>
@@ -53,7 +53,7 @@
             <param name="min_mapq" value="1"/>
             <param name="walks_policy" value="mask"/>
             <param name="max_inter_algn_gap" value="20"/>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
         </test>
         <!--Test 02 with BAM file as input and default parameters-->
         <test expect_num_outputs="1">
@@ -62,7 +62,7 @@
             <param name="min_mapq" value="1"/>
             <param name="walks_policy" value="mask"/>
             <param name="max_inter_algn_gap" value="20"/>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
         </test>
         <!--Test 03 with BAM file as input and minimal mapq of 40-->
         <test expect_num_outputs="1">
@@ -71,7 +71,7 @@
             <param name="min_mapq" value="40"/>
             <param name="walks_policy" value="mask"/>
             <param name="max_inter_algn_gap" value="20"/>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
         </test>
         <!--Test 04 with BAM file as input and walk policy of 5unique-->
         <test expect_num_outputs="1">
@@ -80,7 +80,7 @@
             <param name="min_mapq" value="40"/>
             <param name="walks_policy" value="5unique"/>
             <param name="max_inter_algn_gap" value="20"/>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
         </test>
         <!--Test 05 with BAM file as input and read id dropped-->
         <test expect_num_outputs="1">
@@ -90,7 +90,7 @@
             <param name="walks_policy" value="5unique"/>
             <param name="max_inter_algn_gap" value="20"/>
             <param name="drop_readid" value="true"></param>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
         </test>
         <!--Test 06 with SAM file as input and drop_seq enabled-->
         <test expect_num_outputs="1">
@@ -100,7 +100,7 @@
             <param name="walks_policy" value="5unique"/>
             <param name="max_inter_algn_gap" value="20"/>
             <param name="drop_seq" value="true"></param>
-            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
         </test>
         <!--Test 07 with SAM file as input and output_stats enabled-->
         <test expect_num_outputs="2">