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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f
author galaxy-australia
date Fri, 28 Jun 2024 03:38:39 +0000
parents
children
files README.md dorado_pod5_convert.xml macros.xml test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar test-data/FAL00375_473bf0ed_0.ten_reads.pod5 test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 test-data/dorado_models.loc test-data/reads_in_directories.tar.gz tool-data/dorado_models.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 11 files changed, 251 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,48 @@
+
+## Tool versions
+
+Dorado is distributed on
+[DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech.
+The containers are identified by sha256 hash, but not tagged with a version.
+
+We can still use the containers and display the dorado version by hard-coding
+both dorado version and container hash into the wrapper (see `macros.xml`).
+Unfortunately you have to pull a >6 GB container and run `dorado --version` just
+to check the tool version. This also prevents auto-updates of this wrapper.
+
+You can update the list of models at the same time (see
+below). **You must do this when you update the wrapper**.
+
+## Basecalling models
+
+The models are bundled in the container at `/models` and made available by the
+`dorado_models.loc` file. 
+
+The columns are `value`, `container_hash`, `name` and  `path`.
+
+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.
+
+```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/" $0}' \
+    >> tool-data/dorado_models.loc.sample
+```
+
+The loc file doesn't have a header, so you can keep it sorted.
+
+```bash
+cp tool-data/dorado_models.loc.sample \
+    tool-data/dorado_models.loc.sample.old &&
+sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \
+    > tool-data/dorado_models.loc
+```
+
--- /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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,15 @@
+<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>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">dorado</xref>
+        </xrefs>
+    </xml>
+</macros>
Binary file test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar has changed
Binary file test-data/FAL00375_473bf0ed_0.ten_reads.pod5 has changed
Binary file test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_models.loc	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,58 @@
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Binary file test-data/reads_in_directories.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dorado_models.loc.sample	Fri Jun 28 03:38:39 2024 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="dorado_models" comment_char="#">
+        <columns>value, tool_version, name, path</columns>
+        <file path="tool-data/dorado_models.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Jun 28 03:38:39 2024 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="dorado_models" comment_char="#">
+        <columns>value, tool_version, name, path</columns>
+        <file path="${__HERE__}/test-data/dorado_models.loc" />
+    </table>
+</tables>
\ No newline at end of file