Update dedup.xml

galaxyproject · Mar 27, 2024 · 857c6af · 857c6af
1 parent a8880d8
commit 857c6af
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/tools/pairtools/dedup.xml b/tools/pairtools/dedup.xml
@@ -19,12 +19,12 @@
             --nproc-out \${GALAXY_SLOTS:-4}
     ]]></command>
     <inputs>
-        <param name="pairs_path" type="data" format="pairs,pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file."/>
+        <param name="pairs_path" type="data" format="tabular" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file."/>
         <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the sam entries"></param>
     </inputs>
     <outputs>
-        <data name="output_dedup_pairs" format="pairs,pairsam" label="${tool.name} on ${on_string}: .pairsam"/>
-        <data name="output_dups_pairs" format="pairs,pairsam" label="${tool.name} on ${on_string}: .pairsam"/>
+        <data name="output_dedup_pairs" format="tabular" label="${tool.name} on ${on_string}: .pairsam"/>
+        <data name="output_dups_pairs" format="tabular" label="${tool.name} on ${on_string}: .pairsam"/>
             <filter>output_dups</filter>
         </data>
         <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
@@ -35,22 +35,22 @@
         <!--Test 01 with default parameters-->
         <test expect_num_outputs="1">
             <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
-            <output name="output_dedup_pairs" ftype="pairsam" file="output_dedup_pairs.pairsam" lines_diff="10"/>
+            <output name="output_dedup_pairs" ftype="tabular" file="output_dedup_pairs.pairsam" lines_diff="20"/>
         </test>
         <!--Test 02 mark_dups enabled and output_dups-->
         <test expect_num_outputs="2">
             <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
             <param name="mark_dups" value="true"></param>
-            <output name="output_dedup_pairs" ftype="pairsam" file="output_dedup_pairs_markdups.pairsam" lines_diff="10"/>
-            <output name="output_dups_pairs"  ftype="pairsam" file="output_dups_pairs_markdups.pairsam" lines_diff="10"/>
+            <output name="output_dedup_pairs" ftype="tabular" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
+            <output name="output_dups_pairs"  ftype="tabular" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
         </test>
         <!--Test 03 mark_dups and output_stats enabled-->
         <test expect_num_outputs="2">
             <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
             <param name="mark_dups" value="true"></param>
             <param name="output_stats" value="true"></param>
-            <output name="output_dedup_pairs" ftype="pairsam" file="output_dedup_pairs_markdups.pairsam" lines_diff="10"/>
-            <output name="dedup_pairs_stats"  file="output_dedup_pairs.stats" lines_diff="10"/>
+            <output name="output_dedup_pairs" ftype="tabular" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
+            <output name="dedup_pairs_stats"  file="output_dedup_pairs.stats" lines_diff="20"/>
         </test>
 
     </tests>