diff bam2consensus.xml @ 1:2367d00c5182 draft default tip

"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"

--- a/bam2consensus.xml	Wed Jul 17 17:47:45 2019 -0400
+++ b/bam2consensus.xml	Tue Sep 28 06:12:40 2021 +0000
@@ -12,13 +12,12 @@
         <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
         <requirement type="package" version="6.1">ncurses</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="0.006007">perl-biox-seq</requirement>
-        <requirement type="package" version="1.23">perl-file-which</requirement>
+        <requirement type="package" version="0.008002">perl-biox-seq</requirement>
     </requirements>
 
     <!-- ***************************************************************** -->
 
-    <version_command>bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command>
+    <version_command>perl $__tool_directory__/bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command>
 
     <!-- ***************************************************************** -->
 
@@ -30,7 +29,7 @@
     samtools faidx ref.tmp;
     samtools index in.bam;
 
-    bam2consensus
+    perl $__tool_directory__/bam2consensus
         --ref ref.tmp
         --bam in.bam
         --min_qual $min_qual