Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

changeset 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
files salmonKallistoMtxTo10x.xml
diffstat 1 files changed, 1 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/salmonKallistoMtxTo10x.xml	Fri Nov 08 08:42:44 2019 -0500
+++ b/salmonKallistoMtxTo10x.xml	Fri Nov 08 08:49:38 2019 -0500
@@ -12,8 +12,7 @@
             matrixfile=matrix.mtx;
         fi;
         ln -s ${mtx_file} \$matrixfile;
-        echo -e $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./;
-        $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./
+        $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "\${matrixfile}" "${genes_file}" "${barcodes_file}" ./
 	    ]]></command>
 
     <inputs>