Mercurial > repos > trinity_ctat > abundance_estimation_to_matrix
comparison abundance_estimation_to_matrix.xml @ 6:e673d9dd4928 draft
Changing input format type.
| author | trinity_ctat |
|---|---|
| date | Fri, 29 Sep 2017 11:38:03 -0400 |
| parents | 27fe7db7444b |
| children | deed5e162203 |
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| 5:27fe7db7444b | 6:e673d9dd4928 |
|---|---|
| 3 <description>Join RSEM estimates from multiple samples into a single matrix</description> | 3 <description>Join RSEM estimates from multiple samples into a single matrix</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2.7">python</requirement> | 5 <requirement type="package" version="2.7">python</requirement> |
| 6 <requirement type="package">trinity</requirement> | 6 <requirement type="package">trinity</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <command interpreter="python"> | 8 <command> |
| 9 | 9 <![CDATA[ |
| 10 abundance_estimation_to_matrix_wrapper.py | 10 python abundance_estimation_to_matrix_wrapper.py |
| 11 #for $q in $RSEM_samples | 11 #for $q in $RSEM_samples |
| 12 ${q.file} "${q.column_label}" | 12 ${q.file} "${q.column_label}" |
| 13 #end for | 13 #end for |
| 14 ]]> | |
| 14 | 15 |
| 15 </command> | 16 </command> |
| 16 <inputs> | 17 <inputs> |
| 17 | 18 |
| 18 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> | 19 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> |
| 19 <param name="file" label="Add file" type="data" format="text"/> | 20 <param name="file" label="Add file" type="data" format="txt"/> |
| 20 <param name="column_label" label="column label" type="text" /> | 21 <param name="column_label" label="column label" type="text" /> |
| 21 </repeat> | 22 </repeat> |
| 22 | 23 |
| 23 </inputs> | 24 </inputs> |
| 24 <outputs> | 25 <outputs> |
| 25 <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/> | 26 <data format="txt" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/> |
| 26 <data format="text" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/> | 27 <data format="txt" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/> |
| 27 </outputs> | 28 </outputs> |
| 28 <tests> | 29 <tests> |
| 29 <test> | 30 <test> |
| 30 <repeat name="RSEM_samples"> | 31 <repeat name="RSEM_samples"> |
| 31 <param name="file" value="Sp_ds.RSEM.genes.results" /> | 32 <param name="file" value="Sp_ds.RSEM.genes.results" /> |