# HG changeset patch
# User bgruening
# Date 1587829506 0
# Node ID 2fecdec34a047425173c37ae2f5f5d8a95f2f84a
# Parent  e9db844a896a2ddb292eb481b1e243ab8b17a38b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"

diff -r e9db844a896a -r 2fecdec34a04 macros.xml
--- a/macros.xml	Wed Nov 06 13:52:54 2019 -0500
+++ b/macros.xml	Sat Apr 25 15:45:06 2020 +0000
@@ -4,12 +4,10 @@
     <token name="@IDX_VERSION@">q6</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.0.6">bzip2</requirement>
-            <requirement type="package" version="1.2">seqtk</requirement>
+            <requirement type="package" version="1.3">seqtk</requirement>
             <requirement type="package" version="0.14.1">salmon</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="1.10">samtools</requirement>
             <requirement type="package" version="0.2.0">vpolo</requirement>
-            <requirement type="package" version="1.17.2">numpy</requirement>
             <requirement type="package" version="0.25.1">pandas</requirement>
             <requirement type="package" version="1.3.1">scipy</requirement>
         </requirements>
@@ -286,6 +284,7 @@
             <citation type="doi">10.1038/nmeth.4197</citation>
         </citations>
     </xml>
+    <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
     <token name="@indexing@"><![CDATA[
         mkdir ./index &&
         mkdir ./output &&