# HG changeset patch
# User iuc
# Date 1725765725 0
# Node ID ff7764343c37f96e18763276b6448fab1c90d9a3
# Parent  dae754b6a98b7ad09646e06776e3a1bd934ec8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r dae754b6a98b -r ff7764343c37 macros.xml
--- a/macros.xml	Sat Nov 27 12:28:24 2021 +0000
+++ b/macros.xml	Sun Sep 08 03:22:05 2024 +0000
@@ -5,8 +5,15 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.13</token>
-    <token name="@PROFILE@">20.05</token>
+    <!-- NOTE: for some tools only the version of the requirement but not the
+        tool's version is controlled by the TOOL_VERSION token 
+        (because their version is ahead of the requirement version .. 
+         please only bump the minor version in order to let the requirement
+         version catch up eventually). To find the tools check:
+        `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
+    <token name="@TOOL_VERSION@">1.20</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
@@ -103,7 +110,7 @@
         #end if
     ]]></token>
 
-    <xml name="optional_reference">
+    <xml name="optional_reference" token_help="" token_argument="">
         <conditional name="addref_cond">
             <param name="addref_select" type="select" label="Use a reference sequence">
                 <help>@HELP@</help>
@@ -212,37 +219,7 @@
 
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @misc{SAM_def,
-                title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/},}
-            </citation>
-            <citation type="doi">10.1093/bioinformatics/btp352</citation>
-            <citation type="doi">10.1093/bioinformatics/btr076</citation>
-            <citation type="doi">10.1093/bioinformatics/btr509</citation>
-            <citation type="bibtex">
-                @misc{Danecek_et_al,
-                Author={Danecek, P., Schiffels, S., Durbin, R.},
-                title={Multiallelic calling model in bcftools (-m)},
-                url = {http://samtools.github.io/bcftools/call-m.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Durbin_VCQC,
-                Author={Durbin, R.},
-                title={Segregation based metric for variant call QC},
-                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Li_SamMath,
-                Author={Li, H.},
-                title={Mathematical Notes on SAMtools Algorithms},
-                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{SamTools_github,
-                title={SAMTools GitHub page},
-                url = {https://github.com/samtools/samtools},}
-            </citation>
+            <citation type="doi">10.1093/gigascience/giab008</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r dae754b6a98b -r ff7764343c37 samtools_calmd.xml
--- a/samtools_calmd.xml	Sat Nov 27 12:28:24 2021 +0000
+++ b/samtools_calmd.xml	Sun Sep 08 03:22:05 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_calmd" name="Samtools calmd" version="2.0.3" profile="@PROFILE@">
+<tool id="samtools_calmd" name="Samtools calmd" version="2.0.4" profile="@PROFILE@">
     <description>recalculate MD/NM tags</description>
     <macros>
         <import>macros.xml</import>
diff -r dae754b6a98b -r ff7764343c37 test-data/samtools_calmd_out_1.bam
Binary file test-data/samtools_calmd_out_1.bam has changed
diff -r dae754b6a98b -r ff7764343c37 test-data/samtools_calmd_out_2.bam
Binary file test-data/samtools_calmd_out_2.bam has changed