Mercurial > repos > iuc > samtools_view

comparison samtools_view.xml @ 6:ff313de5f7f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 02:25:30 -0400
parents fdc58a0cc1d4
children b01db2684fa5
comparison
equal deleted inserted replaced
5:90944a49ad05 6:ff313de5f7f4
118 118
119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM 119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
120 ## then sort the output by coordinate, 120 ## then sort the output by coordinate,
121 #if not $input.is_of_type('bam') and $outtype == 'bam': 121 #if not $input.is_of_type('bam') and $outtype == 'bam':
122 && samtools sort 122 && samtools sort
123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
124 -O bam 124 -O bam
125 -o 'tmpsam' 125 -o 'tmpsam'
126 outfile 126 outfile
127 && mv tmpsam outfile 127 && mv tmpsam outfile
128 #if $adv_output.outputpassing == 'yes': 128 #if $adv_output.outputpassing == 'yes':
129 && samtools sort 129 && samtools sort
130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
131 -O bam 131 -O bam
132 -o 'tmpsam' 132 -o 'tmpsam'
133 inv_outfile 133 inv_outfile
134 && mv tmpsam inv_outfile 134 && mv tmpsam inv_outfile
135 #end if 135 #end if
226 <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/> 226 <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
227 </when> 227 </when>
228 <when value="cached"> 228 <when value="cached">
229 <param name="ref" type="select" label="Using reference genome"> 229 <param name="ref" type="select" label="Using reference genome">
230 <options from_data_table="fasta_indexes"> 230 <options from_data_table="fasta_indexes">
231 <filter column="1" key="dbkey" ref="input" type="data_meta" /> 231 <filter column="dbkey" key="dbkey" ref="input" type="data_meta" />
232 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> 232 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
233 </options> 233 </options>
234 </param> 234 </param>
235 </when> 235 </when>
236 </conditional> 236 </conditional>