| Previous changeset 5:81cbb6a4c1ca (2022-03-17) Next changeset 7:9ed6579f52f3 (2023-02-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 |
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modified:
bbmap.xml |
| b |
| diff -r 81cbb6a4c1ca -r 858a65b52cf9 bbmap.xml --- a/bbmap.xml Thu Mar 17 07:44:30 2022 +0000 +++ b/bbmap.xml Tue Jul 05 13:06:30 2022 +0000 |
| b |
| @@ -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> |