# HG changeset patch
# User iuc
# Date 1755115545 0
# Node ID 880d2519963f31cf67bf77c5395fb390ee8e11ee
# Parent  c1c1d894dd3ab4a843aab0b98d34da003c04411c
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0

diff -r c1c1d894dd3a -r 880d2519963f macros.xml
--- a/macros.xml	Fri Jul 25 13:55:10 2025 +0000
+++ b/macros.xml	Wed Aug 13 20:05:45 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 c1c1d894dd3a -r 880d2519963f sort.xml
--- a/sort.xml	Fri Jul 25 13:55:10 2025 +0000
+++ b/sort.xml	Wed Aug 13 20:05:45 2025 +0000
@@ -1,35 +1,53 @@
-<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
     <description>Sort a 4dn pairs/pairsam file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        #if $pairs_path.is_of_type('4dn_pairs.gz') or $pairs_path.is_of_type('4dn_pairsam.gz'):
+            #set $input_link = "input.gz"
+            #set $output_sorted_pairs_link = "sorted_output.gz"
+        #else
+            #set $input_link = "input"
+            #set $output_sorted_pairs_link = "sorted_output"
+        #end if
+        ln -s '$pairs_path' '$input_link' &&
+        ln -s '$output_sorted_pairs' '$output_sorted_pairs_link' &&
         pairtools sort
-            '$pairs_path'
-            -o '$output_sorted_pairs'
+            '$input_link'
+            -o '$output_sorted_pairs_link'
             --nproc-in \${GALAXY_SLOTS:-4}
             --nproc-out \${GALAXY_SLOTS:-4}
     ]]></command>
     <inputs>      
-        <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/>
+        <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" label="Input file" help="Input a 4dn pairs or pairsam file"/>
     </inputs>
     <outputs>
         <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
         </data>
     </outputs>
     <tests>
-        <!--Test default parameters with pairs file-->
+        <!--Test default parameters with pairs file, this us actually a pairsam file-->
         <test expect_num_outputs="1">
-            <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/>
-            <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/>
+            <param name="pairs_path" ftype="4dn_pairsam" value="output_parsed_pairs_bam.pairs"/>
+            <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" ftype="4dn_pairsam" lines_diff="10"/>
         </test>
         <!--Test default parameters with pairsam file-->
         <test expect_num_outputs="1">
-            <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/>
-            <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/>
+            <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
+            <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
         </test>
-
+        <!--Test default parameters with pairsam file compressed output-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
+            <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="10"/>
+        </test>
+        <!--Test default parameters with pairsam file compressed input-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam.gz"/>
+            <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
+        </test>
     </tests>
     <help><![CDATA[
         **Pairtools sort**
diff -r c1c1d894dd3a -r 880d2519963f test-data/output_dedup_pairs_markdups.pairsam.gz
Binary file test-data/output_dedup_pairs_markdups.pairsam.gz has changed
diff -r c1c1d894dd3a -r 880d2519963f test-data/output_parsed_pairs_sam.pairs.gz
Binary file test-data/output_parsed_pairs_sam.pairs.gz has changed
diff -r c1c1d894dd3a -r 880d2519963f test-data/output_parsed_pairs_sam_assemblyname.pairs.gz
Binary file test-data/output_parsed_pairs_sam_assemblyname.pairs.gz has changed
diff -r c1c1d894dd3a -r 880d2519963f test-data/output_sorted_pairs.pairsam.gz
Binary file test-data/output_sorted_pairs.pairsam.gz has changed
diff -r c1c1d894dd3a -r 880d2519963f test-data/pairs_output2.stats.gz
Binary file test-data/pairs_output2.stats.gz has changed