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tximport tool metadata

Miscellaneous

Name: tximport

Description: Summarize transcript-level estimates for gene-level analysis

Id: tximport

Guid: toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.22.0

Version: 1.22.0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.22.0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.20.0

toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/0.1

tximport

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

bioconductor-tximport

1.22.0

package

bioconductor-genomicfeatures

1.46.1

package

r-getopt

1.20.3

package

Additional information about this tool

Command:

#if $gene_id_source_selector.gene_id_source == 'external_file':
    #if $gene_id_source_selector.gff_source_selector.gff_source == 'history':
        #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf':
            ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_gff' mapping.gff &&
        #else:
            ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab &&
        #end if
    #end if
#end if

Rscript '${__tool_directory__}/tximport.R'
--format $input_source_selector.input_source
#if $input_source_selector.input_source == 'none':
    --txIdCol '$input_source_selector.tx_id_col'
    --abundanceCol '$input_source_selector.abundance_col'
    --countsCol '$input_source_selector.counts_col'
    --lengthCol '$input_source_selector.length_col'
#end if
#if $gene_id_source_selector.gene_id_source == 'gene_id_column_option':
    --geneIdCol '$gene_id_source_selector.gene_id_column'
#else
    #if $gene_id_source_selector.gff_source_selector.gff_source == "history":
        #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'tx2gene':
            --tx2gene mapping.tab
        #else
            --gff_file mapping.gff
        #end if
    #else:
        --tx2gene $gene_id_source_selector.gff_source_selector.tx2gene.fields.path
    #end if
#end if
--countsFiles '$counts_files_table'
--countsFromAbundance $counts_from_abundance
--out_file '${gene_level_values}'

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

name: value

salmon_sample2.tab
salmon_sample1.tab
tx2gene.tab
value

Test-2

counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab']
input_source_selector|input_source: salmon
gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|own_gff: Araport11_subset.gff3
gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|mapping_file_option: gff_gtf
gene_id_source_selector|gff_source_selector|gff_source: history
gene_id_source_selector|gene_id_source: external_file
counts_from_abundance: no

name: value

salmon_sample2.tab
salmon_sample1.tab
Araport11_subset.gff3
value

Test-3

counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab']
input_source_selector|input_source: salmon
gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset
gene_id_source_selector|gff_source_selector|gff_source: built-in
gene_id_source_selector|gene_id_source: external_file
counts_from_abundance: no

name: value

salmon_sample2.tab
salmon_sample1.tab
value

Test-4

counts_file: custom_sample.tab
input_source_selector|tx_id_col: Transcript_id_here
input_source_selector|abundance_col: Abundance_goes_here
input_source_selector|counts_col: Here_goes_the_counts
input_source_selector|length_col: Here_goes_the_length
input_source_selector|input_source: none
gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset
gene_id_source_selector|gff_source_selector|gff_source: built-in
counts_from_abundance: no

name: value

custom_sample.tab
value