diff macros.xml @ 13:3fbefde449bc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"

--- a/macros.xml	Fri Sep 17 20:22:27 2021 +0000
+++ b/macros.xml	Thu Nov 18 20:01:04 2021 +0000
@@ -1,10 +1,10 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.3.2</token>
+    <token name="@TOOL_VERSION@">1.4.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="bio_tools">
         <xrefs>
-            <xref type="bio.tools">khmer</xref>
+            <xref type="bio.tools">medaka</xref>
         </xrefs>
     </xml>
     <xml name="requirements">
@@ -52,22 +52,51 @@
         <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@">
+        <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>
+            <option value="r103_fast_variant_g507">r103_fast_variant_g507</option>
+            <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="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
+            <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
+            <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</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="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>
@@ -76,6 +105,9 @@
             <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>
@@ -111,6 +143,28 @@
 
 This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
     ]]></token>
+
+    <token name="@MODELS@"><![CDATA[
+
+----
+
+.. class:: infomark
+
+**Models**
+
+For best results it is important to specify the correct model, -m in the above, according to the basecaller used. Allowed values can be found by running medaka tools list\_models.
+
+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, with the format:
+
+    ::
+
+        {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 
+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://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
     ]]></token>