# HG changeset patch
# User nml
# Date 1667864489 0
# Node ID 2cc9e69419d27ffbc61d52ea972a9e1b0b1377a6
# Parent  4a80a8ffb288d5b37dbe25f89d8c8c8269f78014
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333

diff -r 4a80a8ffb288 -r 2cc9e69419d2 spades_header_fixer.xml
--- a/spades_header_fixer.xml	Fri Sep 02 20:18:41 2022 +0000
+++ b/spades_header_fixer.xml	Mon Nov 07 23:41:29 2022 +0000
@@ -1,9 +1,9 @@
-<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0">
+<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy1">
 	<description>Fixes Spades Fasta ids</description>
   <requirements>
       <requirement type="package" version="4.7.0">sed</requirement>
   </requirements>
-  <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command>
+  <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1_\2/g" $input >$output</command>
 	<inputs>
 		<param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
 		</inputs>
diff -r 4a80a8ffb288 -r 2cc9e69419d2 test-data/spades_header_fixed_1.fasta
--- a/test-data/spades_header_fixed_1.fasta	Fri Sep 02 20:18:41 2022 +0000
+++ b/test-data/spades_header_fixed_1.fasta	Mon Nov 07 23:41:29 2022 +0000
@@ -1,4 +1,4 @@
->spades_before_1.fasta_1 length_792_cov_31.561498
+>spades_before_1.fasta_1_length_792_cov_31.561498
 TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
 TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
 ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG
diff -r 4a80a8ffb288 -r 2cc9e69419d2 test-data/spades_header_fixed_2.fasta
--- a/test-data/spades_header_fixed_2.fasta	Fri Sep 02 20:18:41 2022 +0000
+++ b/test-data/spades_header_fixed_2.fasta	Mon Nov 07 23:41:29 2022 +0000
@@ -1,4 +1,4 @@
->spades_before_2.fasta 00001 len=272039 cov=11.6 corr=0 origname=NODE_1_length_272039_cov_11.639952 sw=shovill-spades/1.0.4 date=20211013
+>spades_before_2.fasta_00001 len=272039 cov=11.6 corr=0 origname=NODE_1_length_272039_cov_11.639952 sw=shovill-spades/1.0.4 date=20211013
 TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
 TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
 ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG