diff medaka_consensus.xml @ 17:d9b6a4615626 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4

--- 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.
 
 ----