Mercurial > repos > dfornika > snippy_clean_full_aln
changeset 4:0bd30a111a55 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/snippy_clean commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
| author | dfornika |
|---|---|
| date | Thu, 30 Jan 2020 00:02:46 +0000 |
| parents | 9dabd403034f |
| children | 201302fa7651 |
| files | snippy_clean_full_aln.xml test-data/core.full.nonclean.aln |
| diffstat | 2 files changed, 55 insertions(+), 3 deletions(-) [+] |
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--- a/snippy_clean_full_aln.xml Fri Jan 24 22:36:09 2020 +0000 +++ b/snippy_clean_full_aln.xml Thu Jan 30 00:02:46 2020 +0000 @@ -10,21 +10,69 @@ <command detect_errors="exit_code"><![CDATA[ snippy-clean_full_aln '${full_aln}' + --to '${to_char}' > '${clean_full_aln}' ]]></command> <inputs> <param name="full_aln" type="data" format="fasta" label="Snippy core.full.aln file" help="" /> + <param name="to_char" type="text" default="N" label="Replacement character" help="Replace non-[AGTCN-] chars with this character" > + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </param> </inputs> - <outputs> <data name="clean_full_aln" format="fasta" label="${tool.name} on ${on_string} cleaned core alignment" /> </outputs> - <tests> + <test> + <param name="full_aln" value="core.full.nonclean.aln" /> + <output name="clean_full_aln"> + <assert_contents> + <has_line line="GCNNGC" /> + </assert_contents> + </output> + </test> + <test> + <param name="full_aln" value="core.full.nonclean.aln" /> + <param name="to_char" value="X" /> + <output name="clean_full_aln"> + <assert_contents> + <has_line line="GCXXGC" /> + </assert_contents> + </output> + </test> </tests> + <help><![CDATA[ + The core.full.aln file is a FASTA formatted multiple sequence alignment file. + It has one sequence for the reference, and one for each sample participating + in the core genome calculation. Each sequence has the same length as the reference + sequence. - <help><![CDATA[ + Character Meaning + ATGC Same as the reference + atgc Different from the reference + - Zero coverage in this sample or a deletion relative to the reference + N Low coverage in this sample (based on --mincov) + X Masked region of reference (from --mask) + n Heterozygous or poor quality genotype (has GT=0/1 or QUAL < --minqual in snps.raw.vcf) + + You can remove all the "weird" characters and replace them with N using this tool. + This is useful when you need to pass it to a tree-building or recombination-removal + tool: + + ``` + % snippy-clean_full_aln core.full.aln > clean.full.aln + % run_gubbins.py -p gubbins clean.full.aln + % snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln + % FastTree -gtr -nt clean.core.aln > clean.core.tree + ``` ]]></help> <expand macro="citations" /> </tool>