# HG changeset patch
# User artbio
# Date 1549825632 18000
# Node ID 243ed53cbc0d860af93ab34ae6f481f223fe164e
# Parent  faf1b3b933f53d0c98c94dce873f20411534faa0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 3ca97a7e1b47e4ca94f65ea4639c5aeabb5ed8b2

diff -r faf1b3b933f5 -r 243ed53cbc0d sr_bowtie_dataset_annotation.xml
--- a/sr_bowtie_dataset_annotation.xml	Sun Feb 10 11:16:59 2019 -0500
+++ b/sr_bowtie_dataset_annotation.xml	Sun Feb 10 14:07:12 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1">
+<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.2">
   <description>by iterative alignments with sRbowtie</description>
   <requirements>
         <requirement type="package" version="1.1.2">bowtie</requirement>
@@ -31,9 +31,9 @@
         genome_aligned=\$(wc -l < matched.fa) &&
         genome_aligned=\$(( \$genome_aligned/2)) &&
         #if $refGenomeSource1.genomeSource == "history":
-            echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output &&
+            echo -e "$refGenomeSource1.ownFile.name\t\${genome_aligned}\n" > $output &&
         #else:
-            echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output &&
+            echo -e "$refGenomeSource1.index.fields.dbkey\t\${genome_aligned}\n" > $output &&
         #end if            
         #set counter = 0
         #for $i in $AdditionalQueries:
@@ -57,7 +57,7 @@
             class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) &&
             class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) &&
             mv temp_class_unmatched.fa class_unmatched.fa &&
-            echo -e "$i.ownFile.name Matched\t\${class_aligned}\n" >> $output &&
+            echo -e "$i.ownFile.name\t\${class_aligned}\n" >> $output &&
         #end for
         remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
         echo -e "Unmatched to previous indexes\t\${remaining}\n" >> $output
diff -r faf1b3b933f5 -r 243ed53cbc0d test-data/sample1_output.tab
--- a/test-data/sample1_output.tab	Sun Feb 10 11:16:59 2019 -0500
+++ b/test-data/sample1_output.tab	Sun Feb 10 14:07:12 2019 -0500
@@ -1,8 +1,8 @@
-2L-tail.fa Matched	2954
+2L-tail.fa	2954
 
-dme_miR21_hairpin.fa Matched	0
+dme_miR21_hairpin.fa	0
 
-Ensembl_transposon_set.fa Matched	2689
+Ensembl_transposon_set.fa	2689
 
 Unmatched to previous indexes	265
 
diff -r faf1b3b933f5 -r 243ed53cbc0d test-data/sample_output.tab
--- a/test-data/sample_output.tab	Sun Feb 10 11:16:59 2019 -0500
+++ b/test-data/sample_output.tab	Sun Feb 10 14:07:12 2019 -0500
@@ -1,8 +1,8 @@
-2L-tail.fa Matched	638
+2L-tail.fa	638
 
-dme_miR21_hairpin.fa Matched	0
+dme_miR21_hairpin.fa	0
 
-Ensembl_transposon_set.fa Matched	560
+Ensembl_transposon_set.fa	560
 
 Unmatched to previous indexes	78