diff split.xml @ 9:7a125af14644 draft

planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0

--- 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>