--- a/samtools_markdup.xml	Mon Aug 15 09:17:57 2022 +0000
+++ b/samtools_markdup.xml	Fri Apr 07 21:47:07 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" >
+<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" >
     <description>marks duplicate alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -85,9 +85,9 @@
         <!-- output bam, if input was name sorted then restore this sorting order -->
         <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}">
             <change_format>
-                <when input="output_format.select_oformat" value="SAM" format="sam" />
-                <when input="output_format.select_oformat" value="BAM" format="bam" />
-                <when input="output_format.select_oformat" value="CRAM" format="cram" />
+                <when input="output_options.output_format.select_oformat" value="SAM" format="sam" />
+                <when input="output_options.output_format.select_oformat" value="BAM" format="bam" />
+                <when input="output_options.output_format.select_oformat" value="CRAM" format="cram" />
             </change_format>
         </data>
         <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics">
@@ -97,31 +97,31 @@
     <tests>
         <!-- 1) -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam" />
             <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 2) -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="2_remove_dups.sam" />
+            <param name="bamfile" value="2_remove_dups.sam" ftype="sam"  />
             <param name="remove" value="-r" />
             <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 3) -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="3_mark_supp_dup.bam" />
+            <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam"  />
             <param name="supp" value="-S" />
             <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 4) test stats output -->
         <test expect_num_outputs="2">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="stats" value="yes" />
             <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
             <output name="stats_output" file="stats.txt" lines_diff="2" />
         </test>
         <!-- 5) check that stderr is not swallowed w test data from fixmate  -->
         <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true">
-            <param name="bamfile" value="3_two_read_mapped.sam" />
+            <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
             <param name="stats" value="yes"/>
             <!-- for some reason this is not possible at the moment
             <output name="stats_output">
@@ -135,35 +135,35 @@
         </test>
         <!-- 6) check optical distance and check -c option -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="odist" value="10" />
             <param name="existing_tags" value="-c" />
             <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 7) check new mode s -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="mode" value="s" />
             <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 8) check include-fails -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="include_fails" value="true" />
             <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 9) test sam format -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="1_markdup.sam" />
+            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="select_oformat" value="SAM" />
-            <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
+            <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
         </test>
         <!-- 10) test cram format -->
         <test expect_num_outputs="1">
-            <param name="bamfile" value="10_markdup.sam" />
+            <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
             <param name="select_oformat" value="CRAM" />
             <param name="ref_file" value="test.fa" />
-            <output name="output" file="10_markdup.expected.cram" compare="sim_size" delta="250"/>
+            <output name="output" file="10_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
         </test>
     </tests>
     <help>