diff dorado_pod5_convert.xml @ 0:18a8d140ec6f draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dorado_pod5_convert.xml	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,60 @@
+<tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>converter for raw Oxford Nanopore data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+
+mkdir input_fast5
+
+&&
+
+tar -xf '$fast5_in' -C input_fast5
+
+&&
+
+pod5 convert fast5
+--threads \${GALAXY_SLOTS:-4}
+--recursive
+--output output.pod5
+input_fast5
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/>
+    </inputs>
+    <outputs>
+        <!-- FIXME: add pod5 datatype to Galaxy and change here.
+        https://github.com/galaxyproject/galaxy/pull/18419 -->
+        <data format="binary" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/>
+            <output name="pod5_out" ftype="binary">
+                <assert_contents>
+                    <has_size value="519736" delta="50000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/>
+            <output name="pod5_out" ftype="binary">
+                <assert_contents>
+                    <has_size value="950136" delta="90000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado.
+
+        Combine all your fast5 files into a single tar archive, and optionally
+        compress the archive with Gzip, Bzip2 or XZ, before uploading it to
+        Galaxy.
+
+            ]]></help>
+</tool>