Galaxy |

Changeset 1:fc5b6491cf78 (2024-07-22)

Previous changeset 0:63d8ecfcfab1 (2024-06-28) Next changeset 2:99c9427219d3 (2024-08-06)

Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit c42b6e3fd2cf6d26e231645a9e8a2986503279e2

modified:
README.md
dorado.xml
macros.xml
test-data/dorado_models.loc
tool-data/dorado_models.loc.sample

diff -r 63d8ecfcfab1 -r fc5b6491cf78 README.md
--- a/README.md Fri Jun 28 03:39:11 2024 +0000
+++ b/README.md Mon Jul 22 04:51:23 2024 +0000

@@ -25,8 +25,8 @@
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"
@@ -34,7 +34,7 @@
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 -r 63d8ecfcfab1 -r fc5b6491cf78 dorado.xml
--- a/dorado.xml Fri Jun 28 03:39:11 2024 +0000
+++ b/dorado.xml Mon Jul 22 04:51:23 2024 +0000

@@ -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 @@

     ]]></command>
     <inputs>
-        
-        <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">
                 
@@ -134,7 +132,7 @@
             </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 -r 63d8ecfcfab1 -r fc5b6491cf78 macros.xml
--- a/macros.xml Fri Jun 28 03:39:11 2024 +0000
+++ b/macros.xml Mon Jul 22 04:51:23 2024 +0000

@@ -1,7 +1,7 @@
<macros>
     
-    <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>

diff -r 63d8ecfcfab1 -r fc5b6491cf78 test-data/dorado_models.loc
--- a/test-data/dorado_models.loc Fri Jun 28 03:39:11 2024 +0000
+++ b/test-data/dorado_models.loc Mon Jul 22 04:51:23 2024 +0000

b'@@ -1,58 +1,59 @@\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_fast@v4.1.0\t/models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_hac@v4.1.0\t/models/dna_r10.4.1_e8.2_260bps_hac@v4.1.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_sup@v4.1.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_sup@v4.1.0\t/models/dna_r10.4.1_e8.2_260bps_sup@v4.1.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.1.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v4.1.0\t/models/dna_r10.4.1_e8.2_400bps_fast@v4.1.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.2.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v4.2.0\t/models/dna_r10.4.1_e8.2_400bps_fast@v4.2.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.3.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v4.3.0\t/models/dna_r10.4.1_e8.2_400bps_fast@v4.3.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v5.0.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_fast@v5.0.0\t/models/dna_r10.4.1_e8.2_400bps_fast@v5.0.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.1.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.1.0\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.1.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.3.0\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2\t1c65eb070a9fc1d88710c4dc09b06541f96fdd28\tdna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2\t/models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2\n-1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0\t1'..b'3cdf1eb2920218\tdna_r9.4.1_e8_fast@v3.4\t/models/dna_r9.4.1_e8_fast@v3.4\n+58b978562389bd0f1842601fb83cdf1eb2920218_dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1\t58b978562389bd0f1842601fb83cdf1eb2920218\tdna_r9.4.1_e8_fast@v3.4_5mCG@v0.1\t/models/dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1\n+58b978562389bd0f1842601fb83cdf1eb2920218_dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0\t58b978562389bd0f1842601fb83cdf1eb2920218\tdna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0\t/models/dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0\n+58b978562389bd0f1842601fb83cdf1eb2920218_dna_r9.4.1_e8_hac@v3.3\t58b978562389bd0f1842601fb83cdf1eb2920218\tdna_r9.4.1_e8_hac@v3.3\t/models/dna_r9.4.1_e8_hac@v3.3\n+58b978562389bd0f1842601fb83cdf1eb2920218_dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1\t58b978562389bd0f1842601fb83cdf1eb2920218\tdna_r9.4.1_e8_hac@v3.3_5mCG@v0.1\t/models/dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1\n+58b978562389bd0f1842601fb83cdf1eb2920218_dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0\t58b978562389bd0f184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diff -r 63d8ecfcfab1 -r fc5b6491cf78 tool-data/dorado_models.loc.sample
--- a/tool-data/dorado_models.loc.sample Fri Jun 28 03:39:11 2024 +0000
+++ b/tool-data/dorado_models.loc.sample Mon Jul 22 04:51:23 2024 +0000