# HG changeset patch # User iuc # Date 1625903114 0 # Node ID a6d65b0c67aff75f0795ead658951074760d0ac6 # Parent 09b2cdb7ace5083f78e1ee3c26b867297b976f4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f" diff -r 09b2cdb7ace5 -r a6d65b0c67af bowtie2_macros.xml --- a/bowtie2_macros.xml Tue Jan 12 16:58:26 2021 +0000 +++ b/bowtie2_macros.xml Sat Jul 10 07:45:14 2021 +0000 @@ -24,7 +24,7 @@ #import itertools #set $input_name1 = $clean($identifier_or_name($input1)) #set $input_name2 = $clean($identifier_or_name($input2)) - #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) + #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))]) #if len($common_prefix) > 3 #return $common_prefix #else diff -r 09b2cdb7ace5 -r a6d65b0c67af bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Tue Jan 12 16:58:26 2021 +0000 +++ b/bowtie2_wrapper.xml Sat Jul 10 07:45:14 2021 +0000 @@ -1,4 +1,4 @@ - + - map reads against reference genome bowtie2_macros.xml @@ -305,9 +305,9 @@ ## output file #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): - | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' + | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' #else if $sam_options.reorder: - | samtools view -bS - -o '$output' + | samtools view --no-PG -bS - -o '$output' #else: > '$output' #end if diff -r 09b2cdb7ace5 -r a6d65b0c67af test-data/bowtie2-test1.bam Binary file test-data/bowtie2-test1.bam has changed diff -r 09b2cdb7ace5 -r a6d65b0c67af test-data/bowtie2-test2.bam Binary file test-data/bowtie2-test2.bam has changed diff -r 09b2cdb7ace5 -r a6d65b0c67af test-data/bowtie2-test_fasta_in.bam Binary file test-data/bowtie2-test_fasta_in.bam has changed diff -r 09b2cdb7ace5 -r a6d65b0c67af test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam Binary file test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam has changed diff -r 09b2cdb7ace5 -r a6d65b0c67af test-data/bowtie2-test_il.bam Binary file test-data/bowtie2-test_il.bam has changed