Mercurial > repos > yboursin > pre_ebseq_eba
changeset 3:954cd01a7c12 draft default tip
Uploaded
| author | yboursin |
|---|---|
| date | Thu, 20 Oct 2016 08:47:19 -0400 |
| parents | 340ada00d965 |
| children | |
| files | EBA_wrapper_preEBSeq.xml |
| diffstat | 1 files changed, 47 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/EBA_wrapper_preEBSeq.xml Thu Oct 20 08:47:19 2016 -0400 @@ -0,0 +1,47 @@ +<tool id="preEBSeq" name="Preprocess files for EBSeq" version="0.1.0"> + <description>Generate expression matrix and IGvector file for EBSeq</description> + <command interpreter="python"> + pre_EBSeq.py + --outtable=$outtable + --outvector=$outvector + #for $i, $input in enumerate ( $batch_condition.levels ): + #for $j, $input_rep in enumerate ($input.rep_counts ): + --inputs "${input_rep.count_data}" "${input_rep.label}" + #end for + #end for + + </command> + <inputs> + <repeat name="rep_counts" title="Raw counts" min="2"> + <param name="count_data" type="data" format="txt" label="Raw count"/> + <param name="label" format="txt" type="text" value="file1" label="File label name" help="You need to specify an unique label name for your replicates."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + </repeat> + + </inputs> + + <outputs> + <data format="tabular" name="outtable" label="Expression matrix (on ${on_string})" /> + <data format="tabular" name="outvector" label="IGvector file (on ${on_string})"/> + </outputs> + <tests> + <test> + + </test> + </tests> + <help> +----------- +Description +----------- +Build Expression Table and IGvector fles from RSEM output to EBSeq input + + </help> +</tool> \ No newline at end of file