diff medaka_variant.xml @ 10:7623e5888be9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

--- a/medaka_variant.xml	Mon Mar 29 20:06:01 2021 +0000
+++ b/medaka_variant.xml	Thu Apr 22 20:24:49 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -41,8 +41,8 @@
         <expand macro="model" argument="-s" label="Select model for initial SNP calling from mixed reads prior to phasing"/>
         <expand macro="model" argument="-m" label="Select model for final variant calling from phased reads"/>
         <expand macro="b"/>
-        <param argument="-N" type="integer" value="14" label="Set threshold for filtering indels in final VCF"/>
-        <param argument="-P" type="integer" value="12" label="Set threshold for filtering SNPs in final VCF"/>
+        <param argument="-N" type="integer" value="9" label="Set threshold for filtering indels in final VCF"/>
+        <param argument="-P" type="integer" value="8" label="Set threshold for filtering SNPs in final VCF"/>
         <param argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Avoid filtering of final VCF?"/>
         <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Stop after initial SNP calling from mixed reads prior to phasing?"/>
         <param name="out" type="select" multiple="true" optional="false" label="Select out file(s)5">
@@ -105,21 +105,21 @@
     <tests>
         <!-- #1 default -->
         <test>
-            <param name="i" value="alignment.bam"/>
+            <param name="i" value="medaka_test.bam"/>
             <conditional name="reference_source">
                 <param name="reference_source_selector" value="cached"/>
-                <param name="ref_file" value="bwa-mem-mt-genome"/>
+                <param name="ref_file" value="ref_fasta"/>
             </conditional>
             <param name="out" value="round_0_hap_mixed_probs.hdf,round_0_hap_mixed_unphased.vcf,log"/>
             <output name="out_round_0_hap_mixed_unphased_vcf">
                 <assert_contents>
-                    <has_n_lines n="6"/>
+                    <has_n_lines n="7"/>
                     <has_line line="##fileformat=VCFv4.1"/>
                 </assert_contents>
             </output>
             <output name="out_round_0_hap_mixed_probs_hdf">
                 <assert_contents>
-                    <has_size value="32624"/>
+                    <has_size value="108753" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_log">