use tar for convert input

tools/dorado/dorado.xml

@@ -28,7 +28,7 @@ calls.bam
 
     ]]></command>
     <inputs>
-        <param name="pod5_file" type="data" format="fast5" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/>
+        <param name="pod5_file" type="data" format="binary" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/>
         <param name="model" type="select" label="Basecalling model. See the Help section for info on model names.">
             <options from_data_table="dorado_models">
                 <!-- only allow models that shipped in this container -->

tools/dorado/dorado_pod5_convert.xml

@@ -6,29 +6,38 @@
     <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command><![CDATA[
-    
-ln -s '$fast5_in' ./input.fast5
+
+mkdir input_fast5
+
+&&
+
+tar -xf '$fast5_in' -C input_fast5
 
 &&
 
 pod5 convert fast5
 --threads \${GALAXY_SLOTS:-4}
+--recursive
 --output output.pod5
-input.fast5 
+input_fast5
 
     ]]>
     </command>
     <inputs>
-        <param name="fast5_in" type="data" format="fast5" label="Oxford Nanopore raw data in fast5 format"/>
+        <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive"/>
     </inputs>
     <outputs>
-        <data format="fast5" name="pod5_out" label="Oxford Nanopore raw data in in pod5 format" from_work_dir="output.pod5"/>
+        <data format="binary" name="pod5_out" label="Oxford Nanopore raw data in in pod5 format" from_work_dir="output.pod5"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="fast5_in" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5"/>
+            <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/>
             <output name="pod5_out" file="dorado_pod5_convert.test1.out.pod5" ftype="fast5"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/>
+            <output name="pod5_out" file="dorado_pod5_convert.test2.out.pod5" ftype="fast5"/>
+        </test>
     </tests>
     <help><![CDATA[
         Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado.