--- a/medaka_variant.xml	Fri Sep 17 20:22:27 2021 +0000
+++ b/medaka_variant.xml	Thu Nov 18 20:01:04 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -91,7 +91,7 @@
         <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
             <filter>'round_1_hap_2_probs_hdf' in out</filter>
         </data>
-        <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf">
+        <data name="out_round_1_phased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf">
             <filter>'round_1_phased.vcf' in out</filter>
         </data>
         <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
@@ -138,6 +138,10 @@
 
 The module *medaka_variant* performs a variant calling via neural networks.
 
+----
+
+.. class:: infomark
+
 **Input**
 
 It is unlikely that the model arguments should be changed from their defaults.
@@ -145,6 +149,10 @@
 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants
 - reference (FASTA)
 
+----
+
+.. class:: infomark
+
 **Output**
 
 - round_0_hap_mixed_phased.bam
@@ -160,6 +168,12 @@
 - round_1.vcf
 - log
 
+@MODELS@
+
+----
+
+.. class:: infomark
+
 **References**
 
 @REFERENCES@