changeset 1:faf1b3b933f5 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit ea052763fe969f830a1ed17e5ffac07146e8d4e9
author artbio
date Sun, 10 Feb 2019 11:16:59 -0500
parents e7e7785e41d0
children 243ed53cbc0d
files sr_bowtie_dataset_annotation.xml
diffstat 1 files changed, 7 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/sr_bowtie_dataset_annotation.xml	Mon Sep 11 18:27:40 2017 -0400
+++ b/sr_bowtie_dataset_annotation.xml	Sun Feb 10 11:16:59 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.0">
+<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1">
   <description>by iterative alignments with sRbowtie</description>
   <requirements>
         <requirement type="package" version="1.1.2">bowtie</requirement>
@@ -30,10 +30,14 @@
                $index_path $format '$input' > tabular_bowtie_output.tab &&
         genome_aligned=\$(wc -l < matched.fa) &&
         genome_aligned=\$(( \$genome_aligned/2)) &&
-        echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output &&
+        #if $refGenomeSource1.genomeSource == "history":
+            echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output &&
+        #else:
+            echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output &&
+        #end if            
         #set counter = 0
         #for $i in $AdditionalQueries:
-            rm genome.fa &&
+            rm -f genome.fa &&
             #set $counter += 1
             #if $counter != 1:
                 #set input = "class_unmatched.fa"