Mercurial > repos > iuc > snippy

annotate snippy_clean_full_aln.xml @ 14:08d22d220254 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit bc5bbb26c53bf2455043cf4b8f552571e6f74530
author iuc
date Mon, 20 Jan 2025 10:10:04 +0000
parents fa016f1eea1a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 <?xml version="1.0" encoding="utf-8"?>
12
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2 <tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
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3 <description>
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4 Replace any non-standard sequence characters in snippy 'core.full.aln' file.
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5 </description>
14
08d22d220254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit bc5bbb26c53bf2455043cf4b8f552571e6f74530
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6 <expand macro="bio_tools"/>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 snippy-clean_full_aln
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13 '${full_aln}'
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14 #if $custom_char.custom_char_selector:
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15 --to '${custom_char.to_char}'
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16 #end if
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17 > '${clean_full_aln}'
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18 ]]></command>
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19
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20 <inputs>
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21 <param name="full_aln" type="data" format="fasta" label="Snippy core.full.aln file" help="" />
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22 <conditional name="custom_char">
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23 <param name="custom_char_selector" type="boolean" display="radio" label="Use custom replacement character" />
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24 <when value="false" />
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25 <when value="true">
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26 <param name="to_char" type="text" label="Replacement character" help="Replace non-[AGTCN-] chars with this character, defaults to 'N' if none entered" >
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27 <sanitizer>
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28 <valid initial="string.printable">
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29 <remove value="&apos;" />
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30 </valid>
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31 <mapping initial="none">
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32 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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33 </mapping>
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34 </sanitizer>
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35 </param>
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="clean_full_aln" format="fasta" label="${tool.name} on ${on_string} cleaned core alignment" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="full_aln" value="core.full.nonclean.aln" />
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45 <output name="clean_full_aln">
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46 <assert_contents>
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47 <has_line line="GCNNCG" />
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <test>
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52 <param name="full_aln" value="core.full.nonclean.aln" />
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53 <param name="custom_char_selector" value="true" />
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54 <param name="to_char" value="X" />
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55 <output name="clean_full_aln">
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56 <assert_contents>
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57 <has_line line="GCXXCG" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 The core.full.aln file is a FASTA formatted multiple sequence alignment file.
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64 It has one sequence for the reference, and one for each sample participating
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65 in the core genome calculation. Each sequence has the same length as the reference
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66 sequence.
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67
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68 Character Meaning
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69 ATGC Same as the reference
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70 atgc Different from the reference
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71 - Zero coverage in this sample or a deletion relative to the reference
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72 N Low coverage in this sample (based on --mincov)
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73 X Masked region of reference (from --mask)
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74 n Heterozygous or poor quality genotype (has GT=0/1 or QUAL < --minqual in snps.raw.vcf)
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75
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76 You can remove all the "weird" characters and replace them with N using this tool.
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77 This is useful when you need to pass it to a tree-building or recombination-removal
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78 tool:
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79
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80 ```
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81 % snippy-clean_full_aln core.full.aln > clean.full.aln
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82 % run_gubbins.py -p gubbins clean.full.aln
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83 % snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln
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84 % FastTree -gtr -nt clean.core.aln > clean.core.tree
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85 ```
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>