diff medaka_consensus.xml @ 13:72b5e9dda577 draft

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

--- a/medaka_consensus.xml	Fri Sep 17 20:23:12 2021 +0000
+++ b/medaka_consensus.xml	Thu Nov 18 20:01:28 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -55,7 +55,7 @@
     <tests>
         <!-- #1 default -->
         <test expect_num_outputs="3">
-            <param name="i" value="basecalls.fastq"/>
+            <param name="i" value="basecalls.fastq.gz"/>
             <param name="d" value="assembly.fasta"/>
             <output name="out_consensus">
                 <assert_contents>
@@ -71,13 +71,13 @@
             </output>
             <output name="out_calls">
                 <assert_contents>
-                    <has_size value="343197" delta="100"/>
+                    <has_size value="343341" delta="100"/>
                 </assert_contents>
             </output>
         </test>
         <!-- #2 -->
         <test expect_num_outputs="5">
-            <param name="i" value="basecalls.fastq"/>
+            <param name="i" value="basecalls.fastq.gz"/>
             <param name="d" value="assembly.fasta"/>
             <param name="m" value="r941_min_fast_g303"/>
             <param name="b" value="99"/>
@@ -95,7 +95,7 @@
             </output>
             <output name="out_calls">
                 <assert_contents>
-                    <has_size value="343197" delta="100"/>
+                    <has_size value="343340" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_log">
@@ -119,10 +119,18 @@
 
 The *medaka_consensus* pipeline performs assembly polishing via neural networks.
 
+----
+
+.. class:: infomark
+
 **Input**
 
 An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these.
 
+----
+
+.. class:: infomark
+
 **Output**
 
 - Consensus polished assembly (FASTA)
@@ -132,6 +140,12 @@
 - Variants: VCF of changes (VCF)
 - Polished: BED file of polished regions (BED)
 
+@MODELS@
+
+----
+
+.. class:: infomark
+
 **References**
 
 @REFERENCES@