# HG changeset patch
# User bgruening
# Date 1571346318 14400
# Node ID 0a5258e41227948607c98f4e034907ed2170a70e
# Parent  e53f19161c59c318f38928417230885818484425
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"

diff -r e53f19161c59 -r 0a5258e41227 alevin.xml
--- a/alevin.xml	Tue Oct 15 12:02:30 2019 -0400
+++ b/alevin.xml	Thu Oct 17 17:05:18 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>