Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x
comparison salmonKallistoMtxTo10x.xml @ 2:40f7a3d18cf4 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 3fbbd818012005da4513271beda50df98d3c1cde-dirty
| author | ebi-gxa |
|---|---|
| date | Fri, 08 Nov 2019 08:32:04 -0500 |
| parents | a2aaefceb418 |
| children | 336ae8f0a0b2 |
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| 1:a2aaefceb418 | 2:40f7a3d18cf4 |
|---|---|
| 2 <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description> | 2 <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package">scipy</requirement> | 4 <requirement type="package">scipy</requirement> |
| 5 <requirement type="package">pandas</requirement> | 5 <requirement type="package">pandas</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command interpreter="python" detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 8 file $mtx_file | grep 'gzip compressed'; | |
| 9 if [ $? -eq 0 ]; then | |
| 10 matrixfile=matrix.mtx.gz; | |
| 11 ln -s ${mtx_file} matrix.mtx.gz; | |
| 12 else | |
| 13 matrixfile=matrix.mtx; | |
| 14 fi; | |
| 15 ln -s ${mtx_file} \$matrixfile; | |
| 8 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ | 16 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ |
| 9 ]]></command> | 17 ]]></command> |
| 10 | 18 |
| 11 <inputs> | 19 <inputs> |
| 12 <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" /> | 20 <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" /> |