Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 3:97ddd78dfa8f draft
Uploaded
author | gkumar09 |
---|---|
date | Wed, 23 Sep 2015 15:21:21 -0400 |
parents | d84c765d4b06 |
children | a40a7ffdf14a |
files | abundance_estimation_to_matrix.xml |
diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance_estimation_to_matrix.xml Wed Sep 23 15:21:21 2015 -0400 @@ -0,0 +1,42 @@ +<tool id="abundance_estimation_to_matrix" name="abundance_estimation_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"> + + abundance_estimation_to_matrix_wrapper.py + #for $q in $RSEM_samples + ${q.file} "${q.column_label}" + #end for + + </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="matrix.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>