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comparison minimap2.xml @ 22:66367287b4e6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 980f7472892817697208792e4443fa579625b696
author iuc
date Tue, 04 Feb 2025 09:17:13 +0000
parents 92678fcb1a5f
children
comparison
equal deleted inserted replaced
21:5cc34c3f440d 22:66367287b4e6
139 #end if 139 #end if
140 $io_options.Y 140 $io_options.Y
141 #if $io_options.K: 141 #if $io_options.K:
142 -K $io_options.K 142 -K $io_options.K
143 #end if 143 #end if
144 #if $io_options.eqx:
145 --eqx
146 #end if
144 -t \${GALAXY_SLOTS:-4} 147 -t \${GALAXY_SLOTS:-4}
145 reference.fa 148 reference.fa
146 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']: 149 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
147 '$fastq_input.fastq_input1' 150 '$fastq_input.fastq_input1'
148 #else if $fastq_input.fastq_input_selector == 'paired': 151 #else if $fastq_input.fastq_input_selector == 'paired':
162 #else if $io_options.output_format == 'CRAM': 165 #else if $io_options.output_format == 'CRAM':
163 | samtools sort 166 | samtools sort
164 -T "\${TMPDIR:-.}" 167 -T "\${TMPDIR:-.}"
165 -@\${GALAXY_SLOTS:-2} 168 -@\${GALAXY_SLOTS:-2}
166 -O $io_options.output_format 169 -O $io_options.output_format
167 $io_options.eqx
168 --reference reference.fa 170 --reference reference.fa
169 --output-fmt-option no_ref 171 --output-fmt-option no_ref
170 -o '$alignment_output' 172 -o '$alignment_output'
171 #else: 173 #else:
172 > '$alignment_output' 174 > '$alignment_output'