Mercurial > repos > nml > refseq_masher

comparison matches.xml @ 1:2c1cb37a3ffe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/refseq_masher commit e83730c5df84a960af58ff09db7eb09d11df2398
author nml
date Wed, 08 May 2019 09:15:56 -0400
parents 26df66c32861
children 1ec42f033bb4
comparison
equal deleted inserted replaced
0:26df66c32861 1:2c1cb37a3ffe
1 <tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.1"> 1 <tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.2">
2 <description> 2 <description>
3 Find closest matching NCBI RefSeq Genomes to your sequences 3 Find closest matching NCBI RefSeq Genomes to your sequences
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.1.1">refseq_masher</requirement> 6 <requirement type="package" version="0.1.1">refseq_masher</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 10
11 #import re 11 #import re
12 #import os
12 13
13 #if $input.type == 'fasta' 14 #if $input.type == 'fasta'
14 #set $input_files = '"{}"'.format($input.fasta.name) 15 #set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0])
15 ln -s "$input.fasta" $input_files && 16 ln -s "$input.fasta" $input_files &&
16 #elif $input.type == 'paired' 17 #elif $input.type == 'paired'
17 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq' 18 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq'
18 #set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext) 19 #set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
19 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq' 20 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'
180 ================================ 181 ================================
181 182
182 Find what NCBI RefSeq genomes most closely match your sequence data using Mash_ with a Mash sketch database of 54,925 NCBI RefSeq Genomes. 183 Find what NCBI RefSeq genomes most closely match your sequence data using Mash_ with a Mash sketch database of 54,925 NCBI RefSeq Genomes.
183 184
184 185
185 Source code available on Github at https://github.com/phac-nml/refseq_masher 186 Source code available on Github at github.com/phac-nml/refseq_masher
186 187
187 188
188 `matches` - find the closest matching NCBI RefSeq Genomes in your input sequences 189 `matches` - find the closest matching NCBI RefSeq Genomes in your input sequences
189 --------------------------------------------------------------------------------- 190 ---------------------------------------------------------------------------------
190 191
215 216
216 With the FNA.GZ_ file for *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_:: 217 With the FNA.GZ_ file for *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_::
217 218
218 219
219 # download sequence file 220 # download sequence file
220 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz 221 wget ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz
221 222
222 # find RefSeq matches 223 # find RefSeq matches
223 refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz 224 refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz
224 225
225 226
266 267
267 Licensed under the Apache License, Version 2.0 (the "License"); you may not use 268 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
268 this work except in compliance with the License. You may obtain a copy of the 269 this work except in compliance with the License. You may obtain a copy of the
269 License at: 270 License at:
270 271
271 http://www.apache.org/licenses/LICENSE-2.0 272 www.apache.org/licenses/LICENSE-2.0
272 273
273 Unless required by applicable law or agreed to in writing, software distributed 274 Unless required by applicable law or agreed to in writing, software distributed
274 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR 275 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
275 CONDITIONS OF ANY KIND, either express or implied. See the License for the 276 CONDITIONS OF ANY KIND, either express or implied. See the License for the
276 specific language governing permissions and limitations under the License. 277 specific language governing permissions and limitations under the License.
278 Contact 279 Contact
279 ------- 280 -------
280 281
281 **Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca 282 **Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca
282 283
283 .. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x 284 .. _Mash: genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
284 .. _FNA.GZ: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz 285 .. _FNA.GZ: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz
285 .. _CHS44: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/ 286 .. _CHS44: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/
286 287
287 288
288 ]]> 289 ]]>
289 </help> 290 </help>
290 <citations> 291 <citations>