Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

comparison salmonKallistoMtxTo10x.xml @ 5:cd6007b47199 draft

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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 08:49:38 -0500
parents 050b51d0f3c4
children 17f7e1e51fad
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4:050b51d0f3c4 5:cd6007b47199
10 matrixfile=matrix.mtx.gz; 10 matrixfile=matrix.mtx.gz;
11 else 11 else
12 matrixfile=matrix.mtx; 12 matrixfile=matrix.mtx;
13 fi; 13 fi;
14 ln -s ${mtx_file} \$matrixfile; 14 ln -s ${mtx_file} \$matrixfile;
15 echo -e $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./; 15 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "\${matrixfile}" "${genes_file}" "${barcodes_file}" ./
16 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./
17 ]]></command> 16 ]]></command>
18 17
19 <inputs> 18 <inputs>
20 <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" /> 19 <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" />
21 <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" /> 20 <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" />