# HG changeset patch
# User iuc
# Date 1725765815 0
# Node ID b6caca6a4ca5121357f3b6317616f69f444e5588
# Parent  eda9f7aa1d5497064f39b9cecb91e5492c9f0758
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r eda9f7aa1d54 -r b6caca6a4ca5 macros.xml
--- a/macros.xml	Mon Aug 15 09:12:10 2022 +0000
+++ b/macros.xml	Sun Sep 08 03:23:35 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 eda9f7aa1d54 -r b6caca6a4ca5 samtools_split.xml
--- a/samtools_split.xml	Mon Aug 15 09:12:10 2022 +0000
+++ b/samtools_split.xml	Sun Sep 08 03:23:35 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>BAM dataset on readgroups</description>
     <macros>
         <import>macros.xml</import>
@@ -8,12 +8,11 @@
     <expand macro="version_command"/>
     <command><![CDATA[
     @ADDTHREADS@
-    samtools split -f 'Read_Group_%!.bam'
+    samtools split -f 'Read_Group_%!.bam' --output-fmt 'bam'
     #if $header:
-        -u '${output}:${header}'
-    #else:
-        -u '${output}'
+        -h $header'
     #end if
+    -u '$output'
     -@ \$addthreads
     '$input_bam'
     ]]></command>
@@ -41,7 +40,7 @@
 
 Splits BAM files on readgroups.
 
-This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
+This tool is based on ``samtools split`` command. It will generate multiple output datasets for each readgroup from the input dataset.
     ]]></help>
     <expand macro="citations"/>
 </tool>
diff -r eda9f7aa1d54 -r b6caca6a4ca5 test-data/phiX_Elephant.bam
Binary file test-data/phiX_Elephant.bam has changed
diff -r eda9f7aa1d54 -r b6caca6a4ca5 test-data/phiX_Human.bam
Binary file test-data/phiX_Human.bam has changed
diff -r eda9f7aa1d54 -r b6caca6a4ca5 test-data/phiX_Mouse.bam
Binary file test-data/phiX_Mouse.bam has changed
diff -r eda9f7aa1d54 -r b6caca6a4ca5 test-data/samtools_split_out.bam
Binary file test-data/samtools_split_out.bam has changed