Mercurial > repos > nml > spades_fasta_header_fixer
comparison spades_header_fixer.xml @ 1:4b00d869c8c0 draft default tip
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333
| author | nml |
|---|---|
| date | Mon, 07 Nov 2022 23:40:55 +0000 |
| parents | c60899ab28a0 |
| children |
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| 0:c60899ab28a0 | 1:4b00d869c8c0 |
|---|---|
| 1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0"> | 1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy1"> |
| 2 <description>Fixes Spades Fasta ids</description> | 2 <description>Fixes Spades Fasta ids</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="4.7.0">sed</requirement> | 4 <requirement type="package" version="4.7.0">sed</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command> | 6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1_\2/g" $input >$output</command> |
| 7 <inputs> | 7 <inputs> |
| 8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> | 8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> |
| 9 </inputs> | 9 </inputs> |
| 10 <outputs> | 10 <outputs> |
| 11 <data name="output" format="fasta"/> | 11 <data name="output" format="fasta"/> |