Mercurial > repos > iuc > medaka_consensus_pipeline

changeset 17:d9b6a4615626 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:58:19 +0000
parents fc8804320156
children
files macros.xml medaka_consensus.xml
diffstat 2 files changed, 64 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Sep 26 10:11:13 2023 +0000
+++ b/macros.xml	Tue Oct 28 09:58:19 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.7.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.1.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="bio_tools">
         <xrefs>
@@ -10,6 +10,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
+            <requirement type="package" version="1.16.2">scipy</requirement>
             <yield />
         </requirements>
     </xml>
@@ -52,8 +53,8 @@
         <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
     </xml>
     <xml name="model" token_argument="-m" token_label="Select model">
-        <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model, 
-            according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION 
+        <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model,
+            according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION
             or PromethION), iii) the basecaller variant, and iv) the basecaller version">
             <option value="r103_fast_g507">r103_fast_g507</option>
             <option value="r103_fast_snp_g507">r103_fast_snp_g507</option>
@@ -61,71 +62,92 @@
             <option value="r103_hac_g507">r103_hac_g507</option>
             <option value="r103_hac_snp_g507">r103_hac_snp_g507</option>
             <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
-            <option value="r103_min_high_g345">r103_min_high_g345</option>
-            <option value="r103_min_high_g360">r103_min_high_g360</option>
-            <option value="r103_prom_high_g360">r103_prom_high_g360</option>
-            <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
-            <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
             <option value="r103_sup_g507">r103_sup_g507</option>
             <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
             <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
+            <option value="r1041_e82_260bps_fast_g632">r1041_e82_260bps_fast_g632</option>
+            <option value="r1041_e82_260bps_fast_variant_g632">r1041_e82_260bps_fast_variant_g632</option>
+            <option value="r1041_e82_260bps_hac_g632">r1041_e82_260bps_hac_g632</option>
+            <option value="r1041_e82_260bps_hac_v4.0.0">r1041_e82_260bps_hac_v4.0.0</option>
+            <option value="r1041_e82_260bps_hac_v4.1.0">r1041_e82_260bps_hac_v4.1.0</option>
+            <option value="r1041_e82_260bps_hac_variant_g632">r1041_e82_260bps_hac_variant_g632</option>
+            <option value="r1041_e82_260bps_hac_variant_v4.1.0">r1041_e82_260bps_hac_variant_v4.1.0</option>
+            <option value="r1041_e82_260bps_joint_apk_ulk_v5.0.0">r1041_e82_260bps_joint_apk_ulk_v5.0.0</option>
+            <option value="r1041_e82_260bps_sup_g632">r1041_e82_260bps_sup_g632</option>
+            <option value="r1041_e82_260bps_sup_v4.0.0">r1041_e82_260bps_sup_v4.0.0</option>
+            <option value="r1041_e82_260bps_sup_v4.1.0">r1041_e82_260bps_sup_v4.1.0</option>
+            <option value="r1041_e82_260bps_sup_variant_g632">r1041_e82_260bps_sup_variant_g632</option>
+            <option value="r1041_e82_260bps_sup_variant_v4.1.0">r1041_e82_260bps_sup_variant_v4.1.0</option>
+            <option value="r1041_e82_400bps_bacterial_methylation">r1041_e82_400bps_bacterial_methylation</option>
             <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
+            <option value="r1041_e82_400bps_fast_g632">r1041_e82_400bps_fast_g632</option>
             <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
+            <option value="r1041_e82_400bps_fast_variant_g632">r1041_e82_400bps_fast_variant_g632</option>
             <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
+            <option value="r1041_e82_400bps_hac_g632">r1041_e82_400bps_hac_g632</option>
+            <option value="r1041_e82_400bps_hac_v4.0.0">r1041_e82_400bps_hac_v4.0.0</option>
+            <option value="r1041_e82_400bps_hac_v4.1.0">r1041_e82_400bps_hac_v4.1.0</option>
+            <option value="r1041_e82_400bps_hac_v4.2.0">r1041_e82_400bps_hac_v4.2.0</option>
+            <option value="r1041_e82_400bps_hac_v4.3.0">r1041_e82_400bps_hac_v4.3.0</option>
+            <option value="r1041_e82_400bps_hac_v5.0.0">r1041_e82_400bps_hac_v5.0.0</option>
+            <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells</option>
+            <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells</option>
+            <option value="r1041_e82_400bps_hac_v5.2.0">r1041_e82_400bps_hac_v5.2.0</option>
+            <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells</option>
+            <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells</option>
             <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
+            <option value="r1041_e82_400bps_hac_variant_g632">r1041_e82_400bps_hac_variant_g632</option>
+            <option value="r1041_e82_400bps_hac_variant_v4.1.0">r1041_e82_400bps_hac_variant_v4.1.0</option>
+            <option value="r1041_e82_400bps_hac_variant_v4.2.0">r1041_e82_400bps_hac_variant_v4.2.0</option>
+            <option value="r1041_e82_400bps_hac_variant_v4.3.0">r1041_e82_400bps_hac_variant_v4.3.0</option>
+            <option value="r1041_e82_400bps_hac_variant_v5.0.0">r1041_e82_400bps_hac_variant_v5.0.0</option>
             <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
+            <option value="r1041_e82_400bps_sup_v4.0.0">r1041_e82_400bps_sup_v4.0.0</option>
+            <option value="r1041_e82_400bps_sup_v4.1.0">r1041_e82_400bps_sup_v4.1.0</option>
+            <option value="r1041_e82_400bps_sup_v4.2.0">r1041_e82_400bps_sup_v4.2.0</option>
+            <option value="r1041_e82_400bps_sup_v4.3.0">r1041_e82_400bps_sup_v4.3.0</option>
+            <option value="r1041_e82_400bps_sup_v5.0.0">r1041_e82_400bps_sup_v5.0.0</option>
+            <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells</option>
+            <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells</option>
+            <option value="r1041_e82_400bps_sup_v5.2.0">r1041_e82_400bps_sup_v5.2.0</option>
+            <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells</option>
+            <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells</option>
             <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
+            <option value="r1041_e82_400bps_sup_variant_v4.1.0">r1041_e82_400bps_sup_variant_v4.1.0</option>
+            <option value="r1041_e82_400bps_sup_variant_v4.2.0">r1041_e82_400bps_sup_variant_v4.2.0</option>
+            <option value="r1041_e82_400bps_sup_variant_v4.3.0">r1041_e82_400bps_sup_variant_v4.3.0</option>
+            <option value="r1041_e82_400bps_sup_variant_v5.0.0">r1041_e82_400bps_sup_variant_v5.0.0</option>
             <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
+            <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
             <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
+            <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
             <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option>
-            <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
-            <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
             <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
-            <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>            
-            <option value="r10_min_high_g303">r10_min_high_g303</option>
-            <option value="r10_min_high_g340">r10_min_high_g340</option>   
+            <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>
+            <option value="r941_e81_fast_g514">r941_e81_fast_g514</option>
             <option value="r941_e81_fast_variant_g514">r941_e81_fast_variant_g514</option>
             <option value="r941_e81_hac_g514">r941_e81_hac_g514</option>
             <option value="r941_e81_hac_variant_g514">r941_e81_hac_variant_g514</option>
             <option value="r941_e81_sup_g514">r941_e81_sup_g514</option>
             <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
-            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
             <option value="r941_min_fast_g507">r941_min_fast_g507</option>
             <option value="r941_min_fast_snp_g507">r941_min_fast_snp_g507</option>
             <option value="r941_min_fast_variant_g507">r941_min_fast_variant_g507</option>
             <option value="r941_min_hac_g507">r941_min_hac_g507</option>
             <option value="r941_min_hac_snp_g507">r941_min_hac_snp_g507</option>
             <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
-            <option value="r941_min_high_g303">r941_min_high_g303</option>
-            <option value="r941_min_high_g330">r941_min_high_g330</option>
-            <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
-            <option value="r941_min_high_g344">r941_min_high_g344</option>
-            <option value="r941_min_high_g351">r941_min_high_g351</option>
-            <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
             <option value="r941_min_sup_g507">r941_min_sup_g507</option>
             <option value="r941_min_sup_snp_g507">r941_min_sup_snp_g507</option>
             <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
-            <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
             <option value="r941_prom_fast_g507">r941_prom_fast_g507</option>
             <option value="r941_prom_fast_snp_g507">r941_prom_fast_snp_g507</option>
             <option value="r941_prom_fast_variant_g507">r941_prom_fast_variant_g507</option>
             <option value="r941_prom_hac_g507">r941_prom_hac_g507</option>
             <option value="r941_prom_hac_snp_g507">r941_prom_hac_snp_g507</option>
             <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
-            <option value="r941_prom_high_g303">r941_prom_high_g303</option>
-            <option value="r941_prom_high_g330">r941_prom_high_g330</option>
-            <option value="r941_prom_high_g344">r941_prom_high_g344</option>
-            <option value="r941_prom_high_g360">r941_prom_high_g360</option>
-            <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
-            <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
-            <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
-            <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
             <option value="r941_prom_sup_g507">r941_prom_sup_g507</option>
             <option value="r941_prom_sup_snp_g507">r941_prom_sup_snp_g507</option>
             <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
-            <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
-            <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
-            <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
             <option value="r941_sup_plant_g610">r941_sup_plant_g610</option>
             <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
         </param>
@@ -177,12 +199,12 @@
 
         {pore}_{device}_{caller variant}_{caller version}
 
-For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model 
+For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model
 r941_prom_hac_g303 should be used with PromethION data and the high accuracy basecaller (termed "hac" in Guppy configuration files). Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
-          
+
     ]]></token>
 
     <token name="@REFERENCES@"><![CDATA[
-More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_.
+More information are available in the `github <https://github.com/nanoporetech/medaka>`_.
     ]]></token>
 </macros>
--- a/medaka_consensus.xml	Tue Sep 26 10:11:13 2023 +0000
+++ b/medaka_consensus.xml	Tue Oct 28 09:58:19 2025 +0000
@@ -16,9 +16,7 @@
 -t \${GALAXY_SLOTS:-4}
 ## required
 -i '$i'
--d 'input_assembly.fa'
-
-2>&1 | tee '$out_log'
+-d 'input_assembly.fa' 2>&1 | tee log.txt
     ]]></command>
     <inputs>
         <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
@@ -49,7 +47,7 @@
             <filter>'gaps' in out</filter>
         </data>
         <!-- optional -->
-        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
+        <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>
@@ -67,7 +65,7 @@
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="169146" delta="100"/>
+                    <has_size value="187317" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
@@ -80,7 +78,7 @@
         <test expect_num_outputs="5">
             <param name="i" value="basecalls.fastq.gz"/>
             <param name="d" value="assembly.fasta"/>
-            <param name="m" value="r941_min_fast_g303"/>
+            <param name="m" value="r941_min_fast_g507"/>
             <param name="b" value="99"/>
             <param name="out" value="consensus,probs,calls,log,gaps"/>
             <output name="out_consensus">
@@ -91,7 +89,7 @@
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="169863" delta="100"/>
+                    <has_size value="187317" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
@@ -126,7 +124,7 @@
 
 **Input**
 
-An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://github.com/nanoporetech/medaka/blob/master/docs/walkthrough.rst>`_ for a detailed example of one method of obtaining these.
+An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required.
 
 ----