Mercurial > repos > bgruening > salmonquantmerge

changeset 3:f6e3a10a88e5 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
author bgruening
date Sat, 25 Apr 2020 11:52:56 -0400
parents 178ebdfe5a7e
children 85b3dc9b6830
files macros.xml
diffstat 1 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Oct 15 12:01:50 2019 -0400
+++ b/macros.xml	Sat Apr 25 11:52:56 2020 -0400
@@ -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 &&