Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 10:adf57ab6155e draft
Uploaded
author | gkumar09 |
---|---|
date | Wed, 23 Sep 2015 15:23:19 -0400 |
parents | 32b2ed082d0c |
children | cad1457c50d2 |
files | diffExpress_edgeR.xml |
diffstat | 1 files changed, 47 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diffExpress_edgeR.xml Wed Sep 23 15:23:19 2015 -0400 @@ -0,0 +1,47 @@ +<tool id="diffExpress_edgeR" name="diffExpress_edgeR" version="0.0.1"> + + <description>Identify Differentially Expressed Transcripts Using EdgeR</description> + <requirements> + <requirement type="package">edgeR</requirement> + </requirements> + <command interpreter="python"> + + trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl + --matrix $counts_matrix + --transcripts $transcripts_fasta_file + --output edgeR_results + --dispersion $dispersion + + > stdout.txt + + + </command> + <inputs> + + <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" /> + <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" /> + <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" /> + + </inputs> + <outputs> + + <data format="txt" name="diff_expressed_edgeR_results" label="${tool.name} on ${on_string}: differentially expressed transcripts per pair of conditions" from_work_dir="edgeR_results/all_diff_expression_results.txt" /> + + <data format="txt" name="matrix_FPKM" label="${tool.name} on ${on_string}: matrix.TMM_normalized.FPKM" from_work_dir="edgeR_results/matrix.TMM_normalized.FPKM" /> + + <data format="txt" name="TMM_info" label="${tool.name} on ${on_string}: TMM library size estimates" from_work_dir="edgeR_results/TMM_info.txt" /> + + </outputs> + <tests> + + <test> + <param name="myname" value="This is just a simple test" /> + + </test> + + + </tests> + <help> + help info here. + </help> +</tool>