Galaxy |

Extract and cluster differentially expressed transcripts tool metadata

Miscellaneous

Name: Extract and cluster differentially expressed transcripts

Description: from a Trinity assembly

Id: trinity_analyze_diff_expr

Guid: toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.5+galaxy2

Version: 2.8.5+galaxy2

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/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.9.1

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.5+galaxy2 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.5+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.3

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.6.6

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.4.0.2

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.4.0.0

toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.2.0.0

trinity_analyze_diff_expr

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

Requirements:

name

version

type

trinity

2.8.5

package

bioconductor-qvalue

2.18.0

package

bioconductor-goseq

1.36.0

package

r-cluster

2.0.8

package

r-fastcluster

1.1.25

package

Functional tests

name

inputs

outputs

required files

Test-1

DE_results: list collection
matrix: count/qcheck/matrix.counts.matrix
samples: count/samples.txt

attributes: name

count/qcheck/matrix.counts.matrix
count/samples.txt
count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
name

Test-2

DE_results: list collection
matrix: count/qcheck/matrix.counts.matrix
samples: count/samples.txt

attributes: name

Test-3

additional_params|GO_enrichment|gene_lengths: count/trinotate/genes.lengths.txt
matrix: count/qcheck/matrix.counts.matrix
additional_params|GO_enrichment|GO_annots: count/trinotate/go_annotations.txt
additional_params|GO_enrichment|examine_GO_enrichment: yes
DE_results: list collection
additional_params|GO_enrichment|DE_matrices: list collection
samples: count/samples.txt

count/qcheck/matrix.counts.matrix
count/samples.txt
count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix
count/trinotate/go_annotations.txt
count/trinotate/genes.lengths.txt