# HG changeset patch
# User ebi-gxa
# Date 1573219924 18000
# Node ID 40f7a3d18cf4ba9e2420caf0b0c5caa062809519
# Parent  a2aaefceb418e8546520c329e44104fbbd0d076d
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 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
@@ -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>