# HG changeset patch
# User iuc
# Date 1725765780 0
# Node ID 84f122ab14d650f8803ad350651b6cbe1aa767db
# Parent  95fd8bf80632db8f96d29233e3b9c18b3acac6a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r 95fd8bf80632 -r 84f122ab14d6 macros.xml
--- a/macros.xml	Mon Aug 15 09:11:35 2022 +0000
+++ b/macros.xml	Sun Sep 08 03:23:00 2024 +0000
@@ -5,8 +5,15 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.15.1</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
@@ -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 95fd8bf80632 -r 84f122ab14d6 samtools_merge.xml
--- a/samtools_merge.xml	Mon Aug 15 09:11:35 2022 +0000
+++ b/samtools_merge.xml	Sun Sep 08 03:23:00 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>merge multiple sorted alignment files</description>
     <macros>
         <import>macros.xml</import>
@@ -38,7 +38,7 @@
 samtools merge
 -@ \$addthreads
 -s $seed
-## TODO force overwrite seems necessay (but I do not understand why ...)
+## force overwrite seems necessay (but I do not understand why ...)
 -f
 ## Galaxy provides only default compression
 ## #if $compression == 'levelone'
@@ -52,14 +52,14 @@
 #if $sortby=='name'
     -n
 #end if
-## TODO since galaxy can't represent this as data type at the moment this option is unsupported
+## since galaxy can't represent this as data type at the moment this option is unsupported
 ## -t TAG    The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
 #if str($region) != ''
     -R '$region'
 #end if
 ## Attach an RG tag to each alignment. The tag value is inferred from file names.
 ## -r
-## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
+## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
 #if $bed_file:
     -L '$bed_file'
 #end if
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diff -r 95fd8bf80632 -r 84f122ab14d6 test-data/3.merge.expected.bam
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diff -r 95fd8bf80632 -r 84f122ab14d6 test-data/4.merge.expected.bam
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diff -r 95fd8bf80632 -r 84f122ab14d6 test-data/5.merge.expected.bam
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diff -r 95fd8bf80632 -r 84f122ab14d6 test-data/6.merge.expected.bam
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