# HG changeset patch
# User iuc
# Date 1569503540 14400
# Node ID 60f888039fb27f63d2a8e562b4e47108630ba80c
# Parent  10c98fab6c5afeaa955ca6386e6d3d1e0a3e74c6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f84c314bc721b5b0c7be10eaf287b1830caca241"

diff -r 10c98fab6c5a -r 60f888039fb2 kallisto_quant.xml
--- a/kallisto_quant.xml	Fri Nov 30 06:26:27 2018 -0500
+++ b/kallisto_quant.xml	Thu Sep 26 09:12:20 2019 -0400
@@ -40,7 +40,7 @@
                 $reads
             #end if
             #if $pseudobam:
-                | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
+                | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' -
             #end if
             && cat run_info.json
         ]]>
diff -r 10c98fab6c5a -r 60f888039fb2 macros.xml
--- a/macros.xml	Fri Nov 30 06:26:27 2018 -0500
+++ b/macros.xml	Thu Sep 26 09:12:20 2019 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.43.1</token>
+    <token name="@VERSION@">0.46.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">kallisto</requirement>
-            <requirement type="package" version="1.5">samtools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 10c98fab6c5a -r 60f888039fb2 test-data/kallisto_pseudo_out1.tab
--- a/test-data/kallisto_pseudo_out1.tab	Fri Nov 30 06:26:27 2018 -0500
+++ b/test-data/kallisto_pseudo_out1.tab	Thu Sep 26 09:12:20 2019 -0400
@@ -1,2 +1,4 @@
-0	0	100
-0	1	100
+%%MatrixMarket matrix coordinate real general
+2	1	2
+1	1	100
+2	1	100
diff -r 10c98fab6c5a -r 60f888039fb2 test-data/kallisto_pseudo_out6.tab
--- a/test-data/kallisto_pseudo_out6.tab	Fri Nov 30 06:26:27 2018 -0500
+++ b/test-data/kallisto_pseudo_out6.tab	Thu Sep 26 09:12:20 2019 -0400
@@ -1,2 +1,4 @@
-0	0	18
-0	1	18
+%%MatrixMarket matrix coordinate real general
+2	1	2
+1	1	18
+2	1	18