Mercurial > repos > nml > spades_fasta_header_fixer
changeset 2:2cc9e69419d2 draft default tip
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333
| author | nml |
|---|---|
| date | Mon, 07 Nov 2022 23:41:29 +0000 |
| parents | 4a80a8ffb288 |
| children | |
| files | spades_header_fixer.xml test-data/spades_header_fixed_1.fasta test-data/spades_header_fixed_2.fasta |
| diffstat | 3 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- 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>
--- 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
--- 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