# HG changeset patch
# User iuc
# Date 1759955180 0
# Node ID 911de3a36b31b1772aaf574b6af7a5eef065704a
# Parent  c19015f577a573cc2b02fa95cf2673531bbedb2e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

diff -r c19015f577a5 -r 911de3a36b31 seqkit_split2.xml
--- a/seqkit_split2.xml	Fri Sep 26 16:48:57 2025 +0000
+++ b/seqkit_split2.xml	Wed Oct 08 20:26:20 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Split sequences into files by part size, number of parts, or length</description>
     <macros>
         <import>macros.xml</import>
@@ -66,14 +66,23 @@
     #end if
     #if str($split_type.split_selector) == 'by_part':
         -p $split_type.by_part
+        #if $paired:
+            --by-part-prefix "seqkit_split2_R{read}_"
+        #end if
     #else if str($split_type.split_selector) == 'by_size':
         -s $split_type.by_size
+        #if $paired:
+            --by-size-prefix string "seqkit_split2_R{read}_"
+        #end if
     #else if str($split_type.split_selector) == 'by_length':
         -l $split_type.by_length
     #end if
     -o seqkit_split2
     -O out
-    -j "\${GALAXY_SLOTS:-4}"
+    -j "\${GALAXY_SLOTS:-4}" 
+    #if $paired:
+        && (find out/ -type f -name "seqkit_split2_*.*" | while read -r file; do mv "\$file" "\$(echo \$file | sed -E 's/(seqkit_split2)_(R1|R2)_([0-9]+)(\..+)/\1_\3_\2\4/' | sed -E 's/_R1/_forward/; s/_R2/_reverse/')"; done)
+    #end if
     ]]></command>
     <inputs>
         <conditional name="input_file_type">
@@ -110,6 +119,11 @@
     <outputs>
         <collection name="outputs_files" type="list" label="${tool.name} on ${on_string}: Splitted files">
             <discover_datasets pattern="(?P&lt;designation&gt;seqkit_split2\.part_\d+)\.(?P&lt;ext&gt;.+)" directory="out"/>
+            <filter>input_file_type['type'] == 'single' </filter>
+        </collection>
+        <collection name="outputs_paired_files" type="list:paired" label="${tool.name} on ${on_string}: Paired-End Splitted files">
+            <filter>input_file_type['type'] == 'paired_collection' </filter>
+                <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_(?P&lt;identifier_1&gt;forward|reverse)\.(?P&lt;ext&gt;.+)" directory="out"/>
         </collection>
     </outputs>
     <tests>
@@ -152,16 +166,30 @@
                 <param name="split_selector" value="by_part"/>
                 <param name="by_part" value="2"/>
             </conditional>
-            <output_collection name="outputs_files" type="list" count="2">
-                <element name="seqkit_split2.part_001" ftype="fastqsanger.gz">
-                    <assert_contents>
-                        <has_n_lines n="4958"/>
-                    </assert_contents>
+            <output_collection name="outputs_paired_files" type="list:paired" count="2">
+                <element name="seqkit_split2_001">
+                    <element name="forward" ftype="fastqsanger.gz">
+                        <assert_contents>
+                            <has_n_lines n="4958"/>
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz">
+                        <assert_contents>
+                            <has_n_lines n="3792"/>
+                        </assert_contents>
+                    </element>    
                 </element>
-                <element name="seqkit_split2.part_002" ftype="fastqsanger.gz">
-                    <assert_contents>
-                        <has_n_lines n="4949"/>
-                    </assert_contents>
+                <element name="seqkit_split2_002">
+                    <element name="forward" ftype="fastqsanger.gz">
+                        <assert_contents>
+                            <has_n_lines n="4949"/>
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz">
+                        <assert_contents>
+                            <has_n_lines n="3657"/>
+                        </assert_contents>  
+                    </element>
                 </element>
             </output_collection>
         </test>