| Previous changeset 1:a2aaefceb418 (2019-11-08) Next changeset 3:336ae8f0a0b2 (2019-11-08) |
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Commit message:
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 |
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modified:
salmonKallistoMtxTo10x.xml |
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| diff -r a2aaefceb418 -r 40f7a3d18cf4 salmonKallistoMtxTo10x.xml --- a/salmonKallistoMtxTo10x.xml Fri Nov 08 08:09:09 2019 -0500 +++ b/salmonKallistoMtxTo10x.xml Fri Nov 08 08:32:04 2019 -0500 |
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| @@ -4,7 +4,15 @@ <requirement type="package">scipy</requirement> <requirement type="package">pandas</requirement> </requirements> - <command interpreter="python" detect_errors="exit_code"><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ + file $mtx_file | grep 'gzip compressed'; + if [ $? -eq 0 ]; then + matrixfile=matrix.mtx.gz; + ln -s ${mtx_file} matrix.mtx.gz; + else + matrixfile=matrix.mtx; + fi; + ln -s ${mtx_file} \$matrixfile; $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ ]]></command> |