Repository revision
2:b91e1e70f3a1

Repository 'pysradb_search'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search

pysradb search tool metadata
Miscellaneous
pysradb search
sequence metadata from SRA/ENA
pysradb_search
toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search/1.4.2+galaxy2
1.4.2+galaxy2
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search/1.4.2+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search/1.4.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search/1.4.2+galaxy0
pysradb_search
Requirements (dependencies defined in the <requirements> tag set)
name version type
pysradb 1.4.2 package
matplotlib 3.6.2 package
imagemagick 7.1.0_52 package
gawk 5.1.0 package
Additional information about this tool
pysradb search
    --db $database
    #if $conditional_platform.instrument
        --query '${conditional_platform.instrument} ${query}'
    #else
        --query '${query}'
    #end if
    --source '${conditional_mode.source}'
    #if $conditional_mode.selector == 'false'
        --organism '${conditional_mode.organism}'
    #end if
    #if $conditional_platform.platform == 'illumina'
        #if $conditional_platform.layout
            --layout $conditional_platform.layout
        #end if
    #end if
    --platform '$conditional_platform.platform'
    #if $selection
        --selection '${selection}'
    #end if
    #if $strategy
        --strategy '${strategy}'
    #end if

    ## Optional fields
    --max $output_options.max
    #if $advanced.mbases
        --mbases $advanced.mbases
    #end if
    #if $advanced.accession
        --accession '${advanced.accession}'
    #end if
    #if $advanced.publication_date
        --publication-date '${advanced.publication_date}'
    #end if
    --verbosity $output_options.verbosity
    #if 'stats' in $output_options.output_files
        --stats
    #end if
    #if 'graphs' in $output_options.output_files
        --graphs 'daterange selection basecount'
    #end if
    --saveto 'output.tsv'
    #if 'stats' in $output_options.output_files
        > stats.txt
        #if $output_options.verbosity == '2' or $output_options.verbosity == '3'
            && echo '  Sequencing instrument:' >> stats.txt
            #if $database == 'sra'
                &&  gawk -F '\t' '{print $11}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print "    ", $0 }' >> stats.txt
            #else
                &&  gawk -F '\t' '{print $12}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print "    ", $0 }' >> stats.txt
            #end if
        #end if
        && echo $'\n  Query keywords: ${query}\n'  >> stats.txt
    #end if
    #if 'graphs' in $output_options.output_files
        && convert 'search_plots/Histogram*.svg' -set filename:fn '%[basename]' 'search_plots/%[filename:fn].jpg'
        && mv 'search_plots/Histogram of Base Count'*.jpg 'search_plots/histogram_base_count.jpg'
        && mv 'search_plots/Histogram of Library'*jpg 'search_plots/histogram_library.jpg'
        && mv 'search_plots/Histogram of Publication'*.jpg 'search_plots/histogram_publication.jpg'
    #end if
None
False
Functional tests
name inputs outputs required files
Test-1 database: sra
query: cancer
conditional_mode|source: transcriptomic
conditional_mode|organism: Homo sapiens
conditional_mode|selector: false
output_options|max: 100
output_options|output_files: ['stats', 'graphs']
 name: value
name: value
 value
Test-2 database: sra
conditional_mode|source: genomic single cell
conditional_mode|organism: Homo sapiens
conditional_mode|selector: false
conditional_platform|instrument: NovaSeq 6000
conditional_platform|platform: illumina
strategy: wga
selection: pcr
advanced|accession: SRX18108950
advanced|publication_date: 01-11-2022
 name: value
name: value
 value
Test-3 database: ena
query: cancer
conditional_mode|source: genomic
conditional_mode|organism: Homo sapiens
conditional_mode|selector: false
strategy: wxs
selection: random
output_options|verbosity: 1
output_options|max: 50
 name: value
name: value
 value
Test-4 database: sra
query: escherichia
conditional_mode|source: metagenomic
conditional_mode|selector: true
advanced|mbases: 100
 name: value
name: value
 value
Test-5 database: sra
query: cancer
conditional_mode|source: transcriptomic
conditional_mode|organism: Homo sapiens
conditional_mode|selector: false
conditional_platform|instrument: MinION
conditional_platform|platform: oxford nanopore
strategy: rna seq
selection: cdna
 name: value
name: value
 value
Test-6 database: sra
query: stress
conditional_mode|source: transcriptomic
conditional_mode|organism: Arabidopsis thaliana
conditional_mode|selector: false
conditional_platform|instrument: NextSeq 500
conditional_platform|platform: illumina
strategy: rna seq
selection: random
output_options|verbosity: 3
output_options|max: 20
 name: value
name: value
 value