--- a/lofreq_viterbi.xml	Fri May 29 19:19:37 2020 +0000
+++ b/lofreq_viterbi.xml	Mon Jun 15 17:11:32 2020 +0000
@@ -1,28 +1,26 @@
-<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy1">
+<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy0">
     <description>with LoFreq viterbi</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
-    </expand>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @PREPARE_REF@
         lofreq viterbi
         --ref '$reference_fasta_fn'
-        ${adv_options.delflags}
+        ${adv_options.keepflags}
         --defqual ${adv_options.bq2_handling.defqual}
         --out tmp.bam '$reads' &&
 
-        samtools sort -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
+        samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
     ]]></command>
     <inputs>
         <param name="reads" type="data" format="bam" label="Reads to realign" />
         <expand macro="reference_interface" />
         <section name="adv_options" title="Advanced options" expanded="false">
-            <param argument="--keepflags" name="delflags" type="boolean" truevalue="" falsevalue="--keepflags" checked="true"
-            label="Delete flags MC, MD, NM, and A?"
-            help="These flags are all prone to getting invalidated during realignment. Keep them only if you know what you are doing." />
+            <param argument="--keepflags" type="boolean" truevalue="--keepflags" falsevalue="" checked="false"
+            label="Keep MC, MD, NM, and A flags?"
+            help="Re-alignment resets the MC, MD, NM, and A flags by default. The values of these tags depend on the exact alignment. Use this option only if you know what you are doing." />
             <conditional name="bq2_handling">
                 <param name="replace_bq2" type="select"
                 label="How to handle base qualities of 2?"
@@ -51,17 +49,18 @@
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
+            <param name="ref_selector" value="history" />
             <param name="ref" ftype="fasta" value="pBR322.fa" />
-            <output name="realigned" file="viterbi-out1.bam" />
+            <output name="realigned" file="viterbi-out1.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
             <section name="adv_options">
-                <param name="delflags" value="false" />
+                <param name="keepflags" value="true" />
             </section>
             <param name="ref" ftype="fasta" value="pBR322.fa" />
-            <output name="realigned" file="viterbi-out2.bam" />
+            <output name="realigned" file="viterbi-out2.bam" ftype="bam" />
         </test>
     </tests>
     <help><![CDATA[