Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 7:a17bb21b711f draft
Uploaded
| author | gkumar09 |
|---|---|
| date | Wed, 23 Sep 2015 15:22:06 -0400 |
| parents | 5fadb4b79378 |
| children | e40d92918044 |
| files | analyze_diff_exp.xml |
| diffstat | 1 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/analyze_diff_exp.xml Wed Sep 23 15:22:06 2015 -0400 @@ -0,0 +1,41 @@ +<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1"> + + <description>Analyze differential expression</description> + <requirements> + <requirement type="package">trinity</requirement> + </requirements> + <command interpreter="python"> + + analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue + + </command> + <inputs> + <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/> + <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" /> + <param name="Pvalue" label="P-value" value="0.05" type="float" /> + <param name="Cvalue" label="C-value" value="0" type="float" /> + + </inputs> + <outputs> + <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/> + <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/> + <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/> + <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + </outputs> + <tests> + + + <test> + <param name="target" value="trinity/Trinity.fasta" /> + <param name="aligner" value="bowtie" /> + <param name="paired_or_single" value="single" /> + <param name="library_type" value="None" /> + <param name="input" value="trinity/reads.left.fq" /> + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>