Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

diff salmonKallistoMtxTo10x.xml @ 2:40f7a3d18cf4 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 08:32:04 -0500
parents a2aaefceb418
children 336ae8f0a0b2
line wrap: on
line diff
--- 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>