Merge pull request #117 from TomHarrop/dorado_bump

Dorado bump
usegalaxy-au · Jul 22, 2024 · c42b6e3 · c42b6e3
2 parents 0e768f0 + 3f7d254
commit c42b6e3
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diff --git a/tools/dorado/README.md b/tools/dorado/README.md
@@ -25,16 +25,16 @@ To update the list, modify `tool-data/dorado_models.loc.sample`.
 Because models can be added and removed, models are listed **per container** in
 the loc file.
 
-Here's some code to **append** the models from the container with hash
-`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`  to the loc file.
+Here's some code to update the loc file with models from the container with hash
+`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`.
 
 ```bash
 export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28"
 
 apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \
     ls /models | \
     awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \
-    >> tool-data/dorado_models.loc.sample
+    > tool-data/dorado_models.loc.sample
 ```
 
 The loc file doesn't have a header, so you can keep it sorted.

diff --git a/tools/dorado/dorado.xml b/tools/dorado/dorado.xml
@@ -1,4 +1,4 @@
-<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1">
     <description>basecaller for raw Oxford Nanopore data</description>
     <macros>
         <import>macros.xml</import>
@@ -28,9 +28,7 @@ calls.bam
 
     ]]></command>
     <inputs>
-        <!-- FIXME: add pod5 datatype to Galaxy and change here.
-        https://github.com/galaxyproject/galaxy/pull/18419 -->
-        <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="pod5_file" type="data" format="pod5" 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 -->
@@ -134,7 +132,7 @@ calls.bam
             </output>
             <output name="out_tsv" ftype="tsv">
                 <assert_contents>
-                    <has_size size="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/>
+                    <has_text text="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/>
                     <has_text text="SQK-RBK114-96_barcode04"/>
                 </assert_contents>
             </output>

diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml
@@ -1,4 +1,4 @@
-<tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1">
     <description>converter for raw Oxford Nanopore data</description>
     <macros>
         <import>macros.xml</import>
@@ -27,22 +27,20 @@ input_fast5
         <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="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
+        <data format="pod5" name="pod5_out" label="${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">
+            <output name="pod5_out" ftype="pod5">
                 <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">
+            <output name="pod5_out" ftype="pod5">
                 <assert_contents>
                     <has_size value="950136" delta="90000"/>
                 </assert_contents>

diff --git a/tools/dorado/macros.xml b/tools/dorado/macros.xml
@@ -1,7 +1,7 @@
 <macros>
     <!-- UPDATING: pull the latest container and check the version. Update both tokens. You MUST also update the model list. See README.md for more.  -->
-    <token name="@VERSION@">0.7.1+80da5f5</token>
-    <token name="@CONTAINER_HASH@">1c65eb070a9fc1d88710c4dc09b06541f96fdd28</token>
+    <token name="@VERSION@">0.7.2+9ac85c6</token>
+    <token name="@CONTAINER_HASH@">58b978562389bd0f1842601fb83cdf1eb2920218</token>
     <xml name="requirements">
         <requirements>
             <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>