# HG changeset patch
# User iuc
# Date 1755115528 0
# Node ID bfb00f8fec97f141ceb7e9708471e1edaff576a2
# Parent  729197476fc17ccb7f890b2d60c083ab2d5a1fc2
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0

diff -r 729197476fc1 -r bfb00f8fec97 macros.xml
--- a/macros.xml	Fri Jul 25 13:54:01 2025 +0000
+++ b/macros.xml	Wed Aug 13 20:05:28 2025 +0000
@@ -1,6 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.1.3</token>
-    <token name="@SUFFIX_VERSION@">1</token>
+    <token name="@SUFFIX_VERSION@">3</token>
+    <token name="@PROFILE_VERSION@">25.0</token>
     <xml name="edam_ontology">
         <edam_datas>
             <edam_data>topic_1381</edam_data>
@@ -29,4 +30,4 @@
         <option value="3unique">3unique - Report the 3'-most unique alignment on each side, if present</option>
         <option value="all">all - Report all available unique alignments on each side</option>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 729197476fc1 -r bfb00f8fec97 parse.xml
--- a/parse.xml	Fri Jul 25 13:54:01 2025 +0000
+++ b/parse.xml	Wed Aug 13 20:05:28 2025 +0000
@@ -1,17 +1,19 @@
-<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy2" profile="23.2" license="MIT">
+<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
     <description>Find ligation pairs in alignments and create pairs.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        #set $output = "output" + str($compress_output)
+        ln -s '$output_parsed_pairs' '$output' &&
         pairtools parse
             '$sam_path'
             -c '$chroms_path'
             #if str($assembly_name).strip(): 
                 --assembly '$assembly_name'
             #end if
-            -o '$output_parsed_pairs'
+            -o '$output'
             --min-mapq '$min_mapq'
             --max-molecule-size '$max_molecule_size'
             $drop_readid
@@ -66,11 +68,16 @@
         </conditional>
         <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
             <expand macro="walks_policy_options"/>
-        </param>   
+        </param>
+        <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output file" />   
         <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
     </inputs>
     <outputs>
-        <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
+        <data name="output_parsed_pairs" format="4dn_pairsam" label="${tool.name} on ${on_string}:  .pairs">
+            <change_format>
+                <when input="compress_output" value=".gz" format="4dn_pairsam.gz"/>
+            </change_format>
+        </data>
         <data name="parsed_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: parsed.stats">
             <filter>output_stats</filter>
         </data>
@@ -83,7 +90,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -92,7 +99,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -101,7 +108,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -110,7 +117,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -120,7 +127,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -130,7 +137,7 @@
             <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="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" 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">
@@ -150,9 +157,20 @@
             <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="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
         </test>
-        <!--Test 09 with SAM file as input and add columns-->
+        <!--Test 09 with SAM file as input and default parameters and assembly name and compressed output--> 
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="assembly_name" value="test_assembly"/>
+            <param name="min_mapq" value="1"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <param name="compress_output" value="true"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.pairs.gz" decompress="true" lines_diff="10"/>
+        </test>
+        <!--Test 10 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"/>
@@ -163,9 +181,8 @@
                 <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"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
         </test>
-
     </tests>
     <help><![CDATA[
         **Pairtools parse**
diff -r 729197476fc1 -r bfb00f8fec97 test-data/output_dedup_pairs_markdups.pairsam.gz
Binary file test-data/output_dedup_pairs_markdups.pairsam.gz has changed
diff -r 729197476fc1 -r bfb00f8fec97 test-data/output_parsed_pairs_sam.pairs.gz
Binary file test-data/output_parsed_pairs_sam.pairs.gz has changed
diff -r 729197476fc1 -r bfb00f8fec97 test-data/output_parsed_pairs_sam_assemblyname.pairs.gz
Binary file test-data/output_parsed_pairs_sam_assemblyname.pairs.gz has changed
diff -r 729197476fc1 -r bfb00f8fec97 test-data/output_sorted_pairs.pairsam.gz
Binary file test-data/output_sorted_pairs.pairsam.gz has changed
diff -r 729197476fc1 -r bfb00f8fec97 test-data/pairs_output2.stats.gz
Binary file test-data/pairs_output2.stats.gz has changed