# HG changeset patch
# User bgruening
# Date 1571346218 14400
# Node ID 519e4b74c149a908b22daa0a3aa499dbb2e0bc5b
# Parent  b579f36923d98ff87333650356af83bb8005b0c4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"

diff -r b579f36923d9 -r 519e4b74c149 alevin.xml
--- a/alevin.xml	Tue Oct 15 12:00:05 2019 -0400
+++ b/alevin.xml	Thu Oct 17 17:03:38 2019 -0400
@@ -7,7 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./index
         && mkdir ./output
-        #if '${refTranscriptSource.TranscriptSource}' != "indexed":
+        #if $refTranscriptSource.TranscriptSource != "indexed":
             && salmon index -i ./index
                 --kmerLen '${refTranscriptSource.s_index.kmer}'
                 --gencode
@@ -149,7 +149,7 @@
     </inputs>
     <outputs>
         <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
-            <filter>not optional["dumpMtx"]</filter>
+            <filter>optional["dumpMtx"] is not True</filter>
         </data>
         <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">
             <filter>optional["dumpMtx"]</filter>