Mercurial > repos > nml > spades_fasta_header_fixer
changeset 0:c60899ab28a0 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
| author | nml |
|---|---|
| date | Fri, 02 Sep 2022 20:18:08 +0000 |
| parents | |
| children | 4b00d869c8c0 |
| files | spades_header_fixer.xml test-data/spades_before_1.fasta test-data/spades_before_2.fasta test-data/spades_header_fixed_1.fasta test-data/spades_header_fixed_2.fasta |
| diffstat | 5 files changed, 99 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spades_header_fixer.xml Fri Sep 02 20:18:08 2022 +0000 @@ -0,0 +1,39 @@ +<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]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command> + <inputs> + <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> + </inputs> + <outputs> + <data name="output" format="fasta"/> + </outputs> + <tests> + <test> + <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> + + <help><![CDATA[ + SPAdes fasta header fixer + ======= + + The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier. + ]]></help> + + <citations> + <citation type="bibtex">@ARTICLE{a1, + title = {SPAdes fasta header fixer}, + author = {Philip Mabon}, + url = {https://github.com/phac-nml/galaxy_tools} + } + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spades_before_1.fasta Fri Sep 02 20:18:08 2022 +0000 @@ -0,0 +1,15 @@ +>NODE_1_length_792_cov_31.561498 +TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG +TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA +ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG +AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG +CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT +TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC +ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT +ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG +CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC +CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT +AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC +GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC +AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spades_before_2.fasta Fri Sep 02 20:18:08 2022 +0000 @@ -0,0 +1,15 @@ +>contig00001 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 +AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG +CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT +TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC +ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT +ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG +CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC +CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT +AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC +GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC +AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spades_header_fixed_1.fasta Fri Sep 02 20:18:08 2022 +0000 @@ -0,0 +1,15 @@ +>spades_before_1.fasta_1 length_792_cov_31.561498 +TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG +TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA +ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG +AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG +CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT +TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC +ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT +ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG +CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC +CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT +AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC +GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC +AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spades_header_fixed_2.fasta Fri Sep 02 20:18:08 2022 +0000 @@ -0,0 +1,15 @@ +>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 +AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG +CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT +TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC +ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT +ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG +CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC +CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT +AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC +GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC +AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG +