# HG changeset patch
# User iuc
# Date 1755115563 0
# Node ID 7a125af14644962b391bb8eb30bc65c615f9dfac
# Parent  0fb51c6f2e37b11e2659b8a434d9a7c357aba20b
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0

diff -r 0fb51c6f2e37 -r 7a125af14644 macros.xml
--- a/macros.xml	Fri Jul 25 13:54:22 2025 +0000
+++ b/macros.xml	Wed Aug 13 20:06:03 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 0fb51c6f2e37 -r 7a125af14644 split.xml
--- a/split.xml	Fri Jul 25 13:54:22 2025 +0000
+++ b/split.xml	Wed Aug 13 20:06:03 2025 +0000
@@ -1,29 +1,44 @@
-<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
     <description>Split a pairsam file into pairs and SAM/BAM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        #if $pairsam_path.is_of_type('4dn_pairsam.gz'):
+            #set $input_link = "input.gz"
+            #set $output_pairs_link = "output_pairs.gz"
+        #else
+            #set $input_link = "input"
+            #set $output_pairs_link = "output_pairs"
+        #end if
+        ln -s '$pairsam_path' '$input_link' &&
+        ln -s '$output_pairs' '$output_pairs_link' &&
         pairtools split
-            '$pairsam_path'
-            --output-pairs '$output_pairs'
+            '$input_link'
+            --output-pairs '$output_pairs_link'
             --output-sam ./output.bam
             --nproc-in \${GALAXY_SLOTS:-4}
             --nproc-out \${GALAXY_SLOTS:-4}
     ]]></command>
     <inputs>
-        <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/>
+        <param name="pairsam_path" type="data" format="4dn_pairsam,4dn_pairsam.gz" label="Input 4dn pairsam file"/>
     </inputs>
     <outputs>
-        <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" />
+        <data name="output_pairs" label="${tool.name} on ${on_string}: Output Pairs"  auto_format="true" />
         <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" />
     </outputs>
     <tests>
         <!--Test default parameters-->
         <test expect_num_outputs="2">
             <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/>
-            <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/>
+            <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs" lines_diff="10"/>
+            <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
+        </test>
+        <!--Test default parameters and compressed input and output-->
+        <test expect_num_outputs="2">
+            <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam.gz"/>
+            <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs.gz" decompress="true" lines_diff="10"/>
             <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
         </test>
     </tests>
diff -r 0fb51c6f2e37 -r 7a125af14644 test-data/output_dedup_pairs_markdups.pairsam.gz
Binary file test-data/output_dedup_pairs_markdups.pairsam.gz has changed
diff -r 0fb51c6f2e37 -r 7a125af14644 test-data/output_parsed_pairs_sam.pairs.gz
Binary file test-data/output_parsed_pairs_sam.pairs.gz has changed
diff -r 0fb51c6f2e37 -r 7a125af14644 test-data/output_parsed_pairs_sam_assemblyname.pairs.gz
Binary file test-data/output_parsed_pairs_sam_assemblyname.pairs.gz has changed
diff -r 0fb51c6f2e37 -r 7a125af14644 test-data/output_sorted_pairs.pairsam.gz
Binary file test-data/output_sorted_pairs.pairsam.gz has changed
diff -r 0fb51c6f2e37 -r 7a125af14644 test-data/pairs_output2.stats.gz
Binary file test-data/pairs_output2.stats.gz has changed