Mercurial > repos > iuc > snippy
changeset 10:3fe8ef358d66 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 25b2375521fec3162644696b67e54f654fab2e79"
| author | iuc |
|---|---|
| date | Thu, 30 Jan 2020 18:18:38 -0500 |
| parents | e4d0231d8595 |
| children | 5bbf9eada9c2 |
| files | snippy_clean_full_aln.xml test-data/core.full.nonclean.aln |
| diffstat | 2 files changed, 91 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy_clean_full_aln.xml Thu Jan 30 18:18:38 2020 -0500 @@ -0,0 +1,87 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@VERSION@+galaxy0"> + <description> + Replace any non-standard sequence characters in snippy 'core.full.aln' file. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + snippy-clean_full_aln + '${full_aln}' + #if $custom_char.custom_char_selector: + --to '${custom_char.to_char}' + #end if + > '${clean_full_aln}' + ]]></command> + + <inputs> + <param name="full_aln" type="data" format="fasta" label="Snippy core.full.aln file" help="" /> + <conditional name="custom_char"> + <param name="custom_char_selector" type="boolean" display="radio" label="Use custom replacement character" /> + <when value="false" /> + <when value="true"> + <param name="to_char" type="text" label="Replacement character" help="Replace non-[AGTCN-] chars with this character, defaults to 'N' if none entered" > + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="clean_full_aln" format="fasta" label="${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="GCNNCG" /> + </assert_contents> + </output> + </test> + <test> + <param name="full_aln" value="core.full.nonclean.aln" /> + <param name="custom_char_selector" value="true" /> + <param name="to_char" value="X" /> + <output name="clean_full_aln"> + <assert_contents> + <has_line line="GCXXCG" /> + </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. + + 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>