# HG changeset patch
# User ebi-gxa
# Date 1573218549 18000
# Node ID a2aaefceb418e8546520c329e44104fbbd0d076d
# Parent  fe0fd27aba50c3caeb02d9d4683652adab8a08e3
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 fe0fd27aba50 -r a2aaefceb418 salmonKallistoMtxTo10x.xml
--- a/salmonKallistoMtxTo10x.xml	Thu Nov 07 05:12:10 2019 -0500
+++ b/salmonKallistoMtxTo10x.xml	Fri Nov 08 08:09:09 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy0">
+<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy1">
     <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
     <requirements>
       <requirement type="package">scipy</requirement>
@@ -9,7 +9,7 @@
 	    ]]></command>
 
     <inputs>
-        <param name="mtx_file" type="data" format="txt" label=".mtx-format matrix" />
+        <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" />
         <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" />
         <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" />
         <param name="cell_prefix" type="text" optional='true' value="" label="Prefix to prepend to cell names / barcodes" help="This is useful when multiple matrices from different libraries with overlapping barcodes will be merged"/>
@@ -18,7 +18,7 @@
     <outputs>
         <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
         <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/>
-        <data name="matrix_out" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
+        <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
     </outputs>
     
     <help><![CDATA[