Mercurial > repos > nml > spades_fasta_header_fixer
diff spades_header_fixer.xml @ 1:4a80a8ffb288 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
| author | nml |
|---|---|
| date | Fri, 02 Sep 2022 20:18:41 +0000 |
| parents | f57f28bdd39b |
| children | 2cc9e69419d2 |
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--- a/spades_header_fixer.xml Thu Dec 19 10:07:39 2019 -0500 +++ b/spades_header_fixer.xml Fri Sep 02 20:18:41 2022 +0000 @@ -1,9 +1,9 @@ -<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1"> +<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0"> <description>Fixes Spades Fasta ids</description> <requirements> <requirement type="package" version="4.7.0">sed</requirement> </requirements> - <command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${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> @@ -12,8 +12,12 @@ </outputs> <tests> <test> - <param name="input" value="spades_before.fasta" /> - <output name="output" file="spades_header_fixed.fasta" ftype="fasta"/> + <param name="input" value="spades_before_1.fasta" /> + <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/> + </test> + <test> + <param name="input" value="spades_before_2.fasta" /> + <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/> </test> </tests>