Workflow: Feature expression merge - combines feature expression from several experiments

Fetched 2023-01-09 01:04:22 GMT

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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Inputs

ID Type Title Doc
alias String Experiment short name/Alias
group_by Group by

Grouping method for features: isoforms, genes or common tss
rpkm_genes File[] (Optional) [TSV] RNA-Seq experiments

CSV/TSV file with RPKM grouped by gene
sample_names String[] RNA-Seq experiments

Aliases for RNA-Seq experiments to be used as the names for the reported columns in the merged file. Order corresponds to the rpkm_genes input

rpkm_isoforms File[] (Optional) [CSV] RNA-Seq experiments

CSV/TSV file with RPKM grouped by isoform
rpkm_common_tss File[] (Optional) [TSV] RNA-Seq experiments

CSV/TSV file with RPKM grouped by common TSS
merge_by_columns String[] (Optional) Columns to merge experiments by

Column names to merge feature files by

Steps

ID Runs Label Doc
feature_merge
../tools/feature-merge.cwl (CommandLineTool)
Feature merge - merges feature files based on the specified columns

Tool merges input feature files based on the columns provided in --mergeby input. All input feature CSV/TSV files should have the header (case-sensitive) Format of the input files is identified based on file's extension *.csv - CSV *.tsv - TSV Otherwise used CSV by default

The output file's rows order corresponds to the rows order of the first CSV/TSV feature file. Output is always saved in TSV format.

Output file includes only rows intersected by column names set in --mergeby. Output file includes only columns set in --mergeby and --report parameters. Column set in the --report parameter is renamed based on the --aliases or basenames of the --features files.

Outputs

ID Type Label Doc
merged_file File [TSV] Merged feature expression file

Merged by merge_by_columns feature expression file

feature_merge_stderr_log File [Textual format] Merging stderr log

Merging stderr log
feature_merge_stdout_log File [Textual format] Merging stdout log

Merging stdout log
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Permalink: https://w3id.org/cwl/view/git/935a78f1aff757f977de4e3672aefead3b23606b/workflows/feature-merge.cwl