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comparison bwa-mem2.xml @ 6:9e5466313f1f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit f7942fbad20a3378a95cb84e90ed14c31c192a4f
author iuc
date Thu, 03 Apr 2025 06:50:28 +0000
parents e25b60805367
children
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5:e25b60805367 6:9e5466313f1f
114 '${reference_fasta_filename}' 114 '${reference_fasta_filename}'
115 '${fastq_input.fastq_input1}' 115 '${fastq_input.fastq_input1}'
116 #end if 116 #end if
117 117
118 #if str( $output_sort ) == "coordinate": 118 #if str( $output_sort ) == "coordinate":
119 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -m "\${GALAXY_MEMORY_MB_PER_SLOT:-768}M" -O bam -o '$bam_output' 119 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
120 #elif str( $output_sort ) == "name": 120 #elif str( $output_sort ) == "name":
121 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -m "\${GALAXY_MEMORY_MB_PER_SLOT:-768}M" -O bam -o '$bam_output' 121 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
122 #else 122 #else
123 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output' 123 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
124 #end if 124 #end if
125 125
126 126