comparison matches.xml @ 1:2c1cb37a3ffe draft

planemo upload for repository https://github.com/phac-nml/refseq_masher commit e83730c5df84a960af58ff09db7eb09d11df2398

0:26df66c32861

<tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.1">
  <description>
    Find closest matching NCBI RefSeq Genomes to your sequences
  </description>
  <requirements>
    <requirement type="package" version="0.1.1">refseq_masher</requirement>
  </requirements>
  <command detect_errors="exit_code">
<![CDATA[

#import re

#if $input.type == 'fasta'
#set $input_files = '"{}"'.format($input.fasta.name)
  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'
#set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
#set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'

================================

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


`matches` - find the closest matching NCBI RefSeq Genomes in your input sequences
---------------------------------------------------------------------------------

With the FNA.GZ_ file for *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_::


    # 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

    # find RefSeq matches
    refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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

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
CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.

Contact
-------

**Gary van Domselaar**: [e-mail]

.. _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/


]]>
  </help>
  <citations>

1:2c1cb37a3ffe

<tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.2">
  <description>
    Find closest matching NCBI RefSeq Genomes to your sequences
  </description>
  <requirements>
    <requirement type="package" version="0.1.1">refseq_masher</requirement>
  </requirements>
  <command detect_errors="exit_code">
<![CDATA[

#import re
#import os

#if $input.type == 'fasta'
#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'
#set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
#set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'

================================

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 github.com/phac-nml/refseq_masher


`matches` - find the closest matching NCBI RefSeq Genomes in your input sequences
---------------------------------------------------------------------------------

With the FNA.GZ_ file for *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_::


    # download sequence file
    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

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this work except in compliance with the License. You may obtain a copy of the
License at:

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
CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.

Contact
-------

**Gary van Domselaar**: [e-mail]

.. _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/


]]>
  </help>
  <citations>