# HG changeset patch
# User ebi-gxa
# Date 1573220978 18000
# Node ID cd6007b47199ae1ff7d18fb91538e31652667684
# Parent  050b51d0f3c46beee21c6b07dd61b3b6ac4d24e5
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

diff -r 050b51d0f3c4 -r cd6007b47199 salmonKallistoMtxTo10x.xml
--- 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>