# HG changeset patch
# User iuc
# Date 1657026274 0
# Node ID c7a39190a385a360aa3b2565973213c6d19fe50f
# Parent  6af1021d16a4da4a3ca10b546a143fdbedd13966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95

diff -r 6af1021d16a4 -r c7a39190a385 bbmap.xml
--- a/bbmap.xml	Thu Mar 17 07:42:30 2022 +0000
+++ b/bbmap.xml	Tue Jul 05 13:04:34 2022 +0000
@@ -137,16 +137,16 @@
     out='all_reads.bam'
     outu='unmapped_reads.bam'
     outm='mapped_reads.bam'
-    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
-    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
-    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
+    && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
+    && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
+    && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
 #elif str($output_options.output_sort) == 'name':
     out='all_reads.bam'
     outu='unmapped_reads.bam'
     outm='mapped_reads.bam'
-    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
-    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
-    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
+    && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
+    && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
+    && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
 #else:
     out='all_reads.bam'
     outu='unmapped_reads.bam'
@@ -269,19 +269,19 @@
             <output name="output_all_reads" ftype="bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="9433" delta="300"/>
+                    <has_size value="9639" delta="300"/>
                 </assert_contents>
             </output>
             <output name="output_unmapped_reads" ftype="bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="9432" delta="300"/>
+                    <has_size value="9639" delta="300"/>
                 </assert_contents>
             </output>
             <output name="output_mapped_reads" ftype="bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="938" delta="100"/>
+                    <has_size value="851" delta="100"/>
                 </assert_contents>
             </output>
         </test>
@@ -294,19 +294,19 @@
             <output name="output_all_reads" ftype="qname_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="17103" delta="600"/>
+                    <has_size value="17540" delta="600"/>
                 </assert_contents>
             </output>
             <output name="output_unmapped_reads" ftype="qname_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="17105" delta="600"/>
+                    <has_size value="17540" delta="600"/>
                 </assert_contents>
             </output>
             <output name="output_mapped_reads" ftype="qname_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="967" delta="100"/>
+                    <has_size value="860" delta="100"/>
                 </assert_contents>
             </output>
         </test>
@@ -325,19 +325,19 @@
             <output name="output_all_reads" ftype="qname_input_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="17059" delta="600"/>
+                    <has_size value="17602" delta="600"/>
                 </assert_contents>
             </output>
             <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="17059" delta="600"/>
+                    <has_size value="17602" delta="600"/>
                 </assert_contents>
             </output>
             <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
                 <metadata name="dbkey" value="89"/>
                 <assert_contents>
-                    <has_size value="906" delta="100"/>
+                    <has_size value="878" delta="100"/>
                 </assert_contents>
             </output>
         </test>