# HG changeset patch
# User ebi-gxa
# Date 1652273740 0
# Node ID 88f5a0a6a8184f0329a8db82ddd21ea23c135ad9
# Parent  e42c217a450f39d7ca5c614046d78143e0e9bd85
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 ec0f8964f4b64fa4d63fba73b9622d7f70b24285

diff -r e42c217a450f -r 88f5a0a6a818 salmonKallistoMtxTo10x.xml
--- a/salmonKallistoMtxTo10x.xml	Wed Mar 11 11:28:41 2020 -0400
+++ b/salmonKallistoMtxTo10x.xml	Wed May 11 12:55:40 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy5" profile="18.01">
+<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy6" profile="18.01">
     <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
     <requirements>
       <requirement type="package" version="1.4.1">scipy</requirement>
@@ -8,9 +8,9 @@
     <command detect_errors="exit_code"><![CDATA[
         file $mtx_file | grep 'gzip compressed' > /dev/null;
         if [ $? -eq 0 ]; then
-            matrixfile=matrix.mtx.gz;
+            matrixfile=matrix-in.mtx.gz;
         else
-            matrixfile=matrix.mtx;
+            matrixfile=matrix-in.mtx;
         fi;
         ln -s ${mtx_file} \$matrixfile;
         $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "\${matrixfile}" "${genes_file}" "${barcodes_file}" ./
@@ -66,5 +66,6 @@
 journal = {GitHub repository},
 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
   }</citation>
+  <citation type="doi">10.1101/2020.04.08.032698</citation>
 </citations>
 </tool>