Mercurial > repos > nml > refseq_masher
diff matches.xml @ 1:2c1cb37a3ffe draft
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 |
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--- a/matches.xml Thu Feb 15 13:59:31 2018 -0500 +++ b/matches.xml Wed May 08 09:15:56 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.1"> +<tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.2"> <description> Find closest matching NCBI RefSeq Genomes to your sequences </description> @@ -9,9 +9,10 @@ <![CDATA[ #import re +#import os #if $input.type == 'fasta' -#set $input_files = '"{}"'.format($input.fasta.name) +#set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0]) ln -s "$input.fasta" $input_files && #elif $input.type == 'paired' #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq' @@ -182,7 +183,7 @@ Find what NCBI RefSeq genomes most closely match your sequence data using Mash_ with a Mash sketch database of 54,925 NCBI RefSeq Genomes. -Source code available on Github at https://github.com/phac-nml/refseq_masher +Source code available on Github at github.com/phac-nml/refseq_masher `matches` - find the closest matching NCBI RefSeq Genomes in your input sequences @@ -217,7 +218,7 @@ # download sequence file - wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz + wget ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz # find RefSeq matches refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz @@ -268,7 +269,7 @@ this work except in compliance with the License. You may obtain a copy of the License at: -http://www.apache.org/licenses/LICENSE-2.0 +www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR @@ -280,9 +281,9 @@ **Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca -.. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x -.. _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 -.. _CHS44: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/ +.. _Mash: genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x +.. _FNA.GZ: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz +.. _CHS44: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/ ]]>