Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 13:8bf618c08b4d draft
Uploaded
| author | gkumar09 |
|---|---|
| date | Wed, 23 Sep 2015 15:24:26 -0400 |
| parents | 895cbd4424a5 |
| children | e2e6533f2514 |
| files | RSEM_estimates_to_matrix.xml |
| diffstat | 1 files changed, 51 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RSEM_estimates_to_matrix.xml Wed Sep 23 15:24:26 2015 -0400 @@ -0,0 +1,51 @@ +<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1"> + + <description>Join RSEM estimates from multiple samples into a single matrix</description> + <requirements> + <requirement type="package">trinity</requirement> + </requirements> + <command interpreter="python"> + + trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl + + --labels + #for $entry in $RSEM_samples: + ${entry.column_label} + #end for + + --RSEM_counts + #for $entry in $RSEM_samples: + ${entry.file} + #end for + + > RSEM.counts.matrix + + </command> + <inputs> + + <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> + <param name="file" label="Add file" type="data" format="text"/> + <param name="column_label" label="column label" type="text" /> + </repeat> + + </inputs> + <outputs> + <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/> + </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>