| Previous changeset 0:26df66c32861 (2018-02-15) Next changeset 2:1ec42f033bb4 (2021-06-25) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/refseq_masher commit e83730c5df84a960af58ff09db7eb09d11df2398 |
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modified:
contains.xml matches.xml |
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| diff -r 26df66c32861 -r 2c1cb37a3ffe contains.xml --- a/contains.xml Thu Feb 15 13:59:31 2018 -0500 +++ b/contains.xml Wed May 08 09:15:56 2019 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="refseq_masher_contains" name="RefSeq Masher Contains" version="0.1.1"> +<tool id="refseq_masher_contains" name="RefSeq Masher Contains" version="0.1.2"> <description> Find NCBI RefSeq Genomes contained in 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' @@ -171,7 +172,7 @@ Find what NCBI RefSeq genomes are contained within 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 `contains` - find what NCBI RefSeq Genomes are contained in your input sequences @@ -217,8 +218,8 @@ We're going to download the FASTQ files for ERR260489_:: - wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_1.fastq.gz - wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_2.fastq.gz + wget ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_1.fastq.gz + wget ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_2.fastq.gz We're going to run `refseq_masher` against these FASTQ files:: @@ -295,7 +296,7 @@ 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 @@ -309,10 +310,10 @@ -.. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x -.. _SAMEA1877340: https://www.ebi.ac.uk/ena/data/view/SAMEA1877340 -.. _PRJEB1775: https://www.ebi.ac.uk/ena/data/view/PRJEB1775 -.. _ERR260489: https://www.ebi.ac.uk/ena/data/view/ERR260489&display=html +.. _Mash: genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x +.. _SAMEA1877340: www.ebi.ac.uk/ena/data/view/SAMEA1877340 +.. _PRJEB1775: www.ebi.ac.uk/ena/data/view/PRJEB1775 +.. _ERR260489: www.ebi.ac.uk/ena/data/view/ERR260489&display=html ]]> </help> |
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| diff -r 26df66c32861 -r 2c1cb37a3ffe matches.xml --- 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/ ]]> |