Mercurial > repos > nml > refseq_masher
diff matches.xml @ 0:26df66c32861 draft
planemo upload commit 80c22275be05e29208e991019309dfffa9704f39
| author | nml |
|---|---|
| date | Thu, 15 Feb 2018 13:59:31 -0500 |
| parents | |
| children | 2c1cb37a3ffe |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matches.xml Thu Feb 15 13:59:31 2018 -0500 @@ -0,0 +1,294 @@ +<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' +#set $_reverse = '"{}_2{}"'.format($re.sub(r'_[12]\..+$', '', $input.reverse.name), $_reverse_ext) +#set $input_files = '{} {}'.format($_forward, $_reverse) + ln -s "$input.forward" $_forward && + ln -s "$input.reverse" $_reverse && +#elif $input.type == 'single' +#set $input_files = '"{}"'.format($input.single.name) + ln -s "$input.single" $input_files && +#elif $input.type == 'paired_collection' +#set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.forward)) else '.fastq' +#set $_forward = '"{}_1{}"'.format($input.paired_collection.name, $_forward_ext) +#set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.reverse)) else '.fastq' +#set $_reverse = '"{}_2{}"'.format($input.paired_collection.name, $_reverse_ext) +#set $input_files = '{} {}'.format($_forward, $_reverse) + ln -s "$input.paired_collection.forward" $_forward && + ln -s "$input.paired_collection.reverse" $_reverse && +#end if + +refseq_masher + $adv.verbosity + matches + --output refseq_masher-matches.${adv.output_type} + --output-type $adv.output_type + --top-n-results $top_n_results +#if $adv.min_kmer_threshold + --min-kmer-threshold $adv.min_kmer_threshold +#end if + -T "\${TMPDIR:-/tmp}" + $input_files +]]> + </command> + <inputs> + <conditional name="input"> + <param name="type" type="select" label="Sequence input type"> + <option value="fasta">Genome FASTA</option> + <option value="paired">Paired-end FASTQs</option> + <option value="single">Single-end FASTQ</option> + <option value="paired_collection">Paired-end FASTQ collection</option> + </param> + <when value="fasta"> + <param name="fasta" + type="data" format="fasta" + optional="false" + label="Genome FASTA file" + /> + </when> + <when value="paired"> + <param name="forward" + type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" + optional="false" + label="Forward FASTQ file" + /> + <param name="reverse" + type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" + optional="false" + label="Reverse FASTQ file" + help="File format must match the Forward FASTQ file" + /> + </when> + <when value="single"> + <param name="single" + type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" + optional="false" + label="Single-end FASTQ file" + /> + </when> + <when value="paired_collection"> + <param name="paired_collection" + type="data_collection" format="fastq,fastqsanger,fastqillumina,fastqsolexa,fastq.gz,txt" + collection_type="paired" + optional="false" + label="Paired-end FASTQ collection" + /> + </when> + </conditional> + <param name="top_n_results" + type="integer" + min="0" + value="20" + optional="true" + label="Top N matches to report (set to 0 to report all)" + /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="min_kmer_threshold" + type="integer" + min="1" + value="8" + optional="true" + label="Mash sketch of reads: Minimum copies of each k-mer required to pass noise filter for reads (default=8)" + /> + <param name="output_type" + type="select" + label="Output type" + multiple="false"> + <option value="tab" selected="true"> + Tabular (tab-delimited values) + </option> + <option value="csv"> + CSV (Comma Separated Values) + </option> + </param> + <param name="verbosity" + type="select" + label="Logging verbosity"> + <option value="">Error messages only</option> + <option value="-v">Show warning messages</option> + <option value="-vv" selected="true">Show info messages</option> + <option value="-vvv">Show debug messages</option> + </param> + </section> + </inputs> + <outputs> + <data name="output_path_csv" + format="csv" + label="RefSeq Masher matches table" + from_work_dir="refseq_masher-matches.csv"> + <filter>adv['output_type'] == 'csv'</filter> + </data> + <data name="output_path_tab" + format="tabular" + label="RefSeq Masher matches table" + from_work_dir="refseq_masher-matches.tab"> + <filter>adv['output_type'] == 'tab'</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="input"> + <param name="type" value="fasta"/> + <param name="fasta" value="Se-Enteritidis.fasta"/> + </conditional> + <param name="top_n_results" value="1"/> + <section name="adv"> + <param name="output_type" value="tab"/> + </section> + <output name="output_path_tab" + value="Se-Enteritidis-refseq_masher-matches.tab" + ftype="tabular" + lines_diff="0"> + </output> + </test> + <test> + <conditional name="input"> + <param name="type" value="single"/> + <param name="single" value="SRR1203042_1-head4000.fastq"/> + </conditional> + <param name="top_n_results" value="1"/> + <section name="adv"> + <param name="output_type" value="tab"/> + <param name="min_kmer_threshold" value="2"/> + </section> + <output name="output_path_tab" + value="SRR1203042_1-head4000-refseq_masher-matches-m2.tab" + ftype="tabular" + lines_diff="0"> + </output> + </test> + </tests> + <help> +<![CDATA[ +RefSeq Masher - Genomic Distance +================================ + +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 +--------------------------------------------------------------------------------- + +Command-line usage information:: + + Usage: refseq_masher matches [OPTIONS] INPUT... + + Find NCBI RefSeq genome matches for an input genome fasta file + + Input is expected to be one or more FASTA/FASTQ files or one or more + directories containing FASTA/FASTQ files. Files can be Gzipped. + + Options: + --mash-bin TEXT Mash binary path (default="mash") + -o, --output PATH Output file path (default="-"/stdout) + --output-type [tab|csv] Output file type (tab|csv) + -n, --top-n-results INTEGER Output top N results sorted by distance in + ascending order (default=5) + -m, --min-kmer-threshold INTEGER + Mash sketch of reads: "Minimum copies of + each k-mer required to pass noise filter for + reads" (default=8) + -h, --help Show this message and exit. + + +Example +~~~~~~~ + +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 + + +**Log**:: + + + 2018-01-29 11:02:13,786 INFO: Collected 1 FASTA inputs and 0 read sets [in ...refseq_masher/refseq_masher/utils.py:185] + 2018-01-29 11:02:13,786 INFO: Creating Mash sketch file for ...refseq_masher/GCF_000329025.1_ASM32902v1_genomic.fna.gz [in ...refseq_masher/refseq_masher/mash/sketch.py:24] + 2018-01-29 11:02:14,055 INFO: Created Mash sketch file at "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/sketch.py:40] + 2018-01-29 11:02:14,613 INFO: Ran Mash dist successfully (output length=11647035). Parsing Mash dist output [in ...refseq_masher/refseq_masher/mash/dist.py:64] + 2018-01-29 11:02:15,320 INFO: Parsed Mash dist output into Pandas DataFrame with 54924 rows [in ...refseq_masher/refseq_masher/mash/dist.py:67] + 2018-01-29 11:02:15,321 INFO: Deleting temporary sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/dist.py:72] + 2018-01-29 11:02:15,321 INFO: Sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" deleted! [in ...refseq_masher/refseq_masher/mash/dist.py:74] + 2018-01-29 11:02:15,322 INFO: Ran Mash dist on all input. Merging NCBI taxonomic information into results output. [in ...refseq_masher/refseq_masher/cli.py:88] + 2018-01-29 11:02:15,323 INFO: Fetching all taxonomy info for 5 unique NCBI Taxonomy UIDs [in ...refseq_masher/refseq_masher/taxonomy.py:35] + 2018-01-29 11:02:15,325 INFO: Dropping columns with all NA values (ncol=32) [in ...refseq_masher/refseq_masher/taxonomy.py:38] + 2018-01-29 11:02:15,327 INFO: Columns with all NA values dropped (ncol=11) [in ...refseq_masher/refseq_masher/taxonomy.py:40] + 2018-01-29 11:02:15,327 INFO: Merging Mash results with relevant taxonomic information [in ...refseq_masher/refseq_masher/taxonomy.py:41] + 2018-01-29 11:02:15,329 INFO: Merged Mash results with taxonomy info [in ...refseq_masher/refseq_masher/taxonomy.py:43] + 2018-01-29 11:02:15,329 INFO: Merged taxonomic info into results output [in ...refseq_masher/refseq_masher/cli.py:90] + 2018-01-29 11:02:15,329 INFO: Reordering output columns [in ...refseq_masher/refseq_masher/cli.py:91] + 2018-01-29 11:02:15,331 INFO: Writing output to stdout [in ...refseq_masher/refseq_masher/writers.py:16] + + +**Output** + ++---------------------------------------+--------------------------------------------------------------------+----------+--------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------+---------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+-------------+---------+-------------+--------------+--------+---------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| sample | top_taxonomy_name | distance | pvalue | matching | full_taxonomy | taxonomic_subspecies | taxonomic_species | taxonomic_genus | taxonomic_family | taxonomic_order | taxonomic_class | taxonomic_phylum | taxonomic_superkingdom | subspecies | serovar | plasmid | bioproject | biosample | taxid | assembly_accession | match_id | ++=======================================+====================================================================+==========+========+==========+=============================================================================================================================================================+=====================================+=====================+==================+====================+==================+=====================+===================+=========================+============+=============+=========+=============+==============+========+=====================+==========================================================================================================================================+ +| GCF_000329025.1_ASM32902v1_genomic | Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 | 0.0 | 0.0 | 400/400 | Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Enteritidis; str. CHS44 | Salmonella enterica subsp. enterica | Salmonella enterica | Salmonella | Enterobacteriaceae | Enterobacterales | Gammaproteobacteria | Proteobacteria | Bacteria | enterica | Enteritidis | | PRJNA185053 | SAMN01041154 | 702979 | NZ_ALFF | ./rcn/refseq-NZ-702979-PRJNA185053-SAMN01041154-NZ_ALFF-.-Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._CHS44.fna | ++---------------------------------------+--------------------------------------------------------------------+----------+--------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------+---------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+-------------+---------+-------------+--------------+--------+---------------------+------------------------------------------------------------------------------------------------------------------------------------------+ + + +The top match is *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_ with a distance of 0.0 and 400/400 sketches matching, which is what we expected. There's other taxonomic information available in the results table that may be useful. + + + +Legal +----- + +Copyright Government of Canada 2017 + +Written by: National Microbiology Laboratory, Public Health Agency of Canada + +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**: 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/ + + +]]> + </help> + <citations> + <!-- Citation for Mash paper --> + <citation type="doi">10.1186/s13059-016-0997-x</citation> + </citations> +</tool>