Repository revision
22:ba3720d7e68b

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

Build expression matrix tool metadata
Miscellaneous
for a de novo assembly of RNA-Seq data by Trinity
trinity_abundance_estimates_to_matrix
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.15.1+galaxy0
2.15.1+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.15.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.9.1
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.5
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.3
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.6.6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.4.0.2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.4.0.1
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.4.0.0
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.2.0.1
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.2.0.0
trinity_abundance_estimates_to_matrix
Requirements (dependencies defined in the <requirements> tag set)
name version type
trinity 2.15.1 package
Additional information about this tool
#import re
        #for $entry in $samples:
            ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
        #end for

        abundance_estimates_to_matrix.pl

        --est_method ${est_method}
        --cross_sample_norm ${additional_params.cross_sample_norm}

        #if $gene_trans_map:
            --gene_trans_map '$gene_trans_map'
        #else:
            --gene_trans_map 'none'
        #end if

        #for $entry in $samples:
            '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
        #end for

        && mv *.isoform.counts.matrix '$trans_counts'
        && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm'
        #if $gene_trans_map:
            && mv *.gene.counts.matrix '$trans_counts_gene'
            && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene'
        #end if

        #if $additional_params.cross_sample_norm == "TMM":
            && mv *.isoform.TMM.EXPR.matrix '$norm_TMM'
            #if $gene_trans_map:
                && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene'
            #end if
        #else if $additional_params.cross_sample_norm == "UpperQuartile":
            && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ'
            #if $gene_trans_map:
                && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
            #end if
        #end if
    
None
False
Functional tests
name inputs outputs required files
Test-1 samples: ['count/rsem_bowtie/sample_A', 'count/rsem_bowtie/sample_B']
est_method: RSEM
additional_params|cross_sample_norm: TMM
name: value
name: value
name: value
count/rsem_bowtie/sample_A
count/rsem_bowtie/sample_B
value
Test-2 samples: ['count/rsem_bowtie2/sample_A', 'count/rsem_bowtie2/sample_B']
est_method: RSEM
additional_params|cross_sample_norm: TMM
name: value
name: value
name: value
count/rsem_bowtie2/sample_A
count/rsem_bowtie2/sample_B
value
Test-3 samples: ['count/express_bowtie/sample_A', 'count/express_bowtie/sample_B']
est_method: eXpress
additional_params|cross_sample_norm: TMM
name: value
name: value
name: value
count/express_bowtie/sample_A
count/express_bowtie/sample_B
value
Test-4 samples: ['count/rsem_bowtie/sample_A', 'count/rsem_bowtie/sample_B']
est_method: RSEM
additional_params|cross_sample_norm: UpperQuartile
name: value
name: value
name: value
count/rsem_bowtie/sample_A
count/rsem_bowtie/sample_B
value
Test-5 samples: ['count/rsem_bowtie/sample_A', 'count/rsem_bowtie/sample_B']
est_method: RSEM
additional_params|cross_sample_norm: none
name: value
name: value
count/rsem_bowtie/sample_A
count/rsem_bowtie/sample_B
value
Test-6 samples: ['count/salmon/sample_A', 'count/salmon/sample_B']
est_method: salmon
additional_params|cross_sample_norm: none
name: value
name: value
count/salmon/sample_A
count/salmon/sample_B
value
Test-7 samples: ['count/kallisto/abundance.tsv.genes', 'count/kallisto/abundance_B.tsv.genes']
est_method: kallisto
additional_params|cross_sample_norm: TMM
name: value
name: value
name: value
count/kallisto/abundance.tsv.genes
count/kallisto/abundance_B.tsv.genes
value