Mercurial > repos > nml > positions2snv_invariant_alignment

annotate positions2snv_invariant_alignment.xml @ 0:bf542eece94a draft

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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author nml
date Tue, 27 Aug 2019 12:32:37 -0400
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children 5dc704146cc6
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bf542eece94a "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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1 <tool id="positions2snv_invariant_alignment" name="Positions to SNV invariant alignment" version ="1.8.2">
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2 <description>Create a SNV and non-variant alignment from the SNVPhyl positions table and a reference genome.</description>
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3 <requirements>
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4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 positions2snv_invariant_alignment.pl -i $snv_table --reference-file $reference_genome -o outputs -f $out_format $keep_all $merge_alignment
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8 ]]></command>
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9 <inputs>
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10 <param name="snv_table" type="data" label="SNV table" format="tabular"/>
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11 <param name="reference_genome" type="data" label="Reference genome" format="fasta"/>
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12 <param name="out_format" type="select" label="Output alignment format">
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13 <option value="phylip">Phylip alignment format</option>
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14 <option value="fasta">FASTA alignment format</option>
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15 </param>
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16 <param name="merge_alignment" type="boolean" checked="false" label="Merge alignment to single file"
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17 help="Merge individual sequences in reference file to single sequence in final alignment" truevalue="--merge-alignment" falsevalue="" />
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18 <param name="keep_all" type="boolean" checked="false" label="Keep all positions"
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19 help="Keep all positions with status 'filtered' in the SNV alignment" truevalue="--keep-all" falsevalue="" />
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20 </inputs>
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21 <outputs>
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22 <collection name="alignments" type="list" label="Alignment files">
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23 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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24 </collection>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="snv_table" value="positions.tsv"/>
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29 <param name="reference_genome" value="reference.fasta"/>
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30 <param name="out_format" value="fasta"/>
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31 <param name="merge_alignment" value="true" />
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32
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33 <output_collection name="alignments" type="list">
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34 <element name="alignment_merged" file="expected-merged.fasta"/>
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35 </output_collection>
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36 </test>
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37 <test>
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38 <param name="snv_table" value="positions.tsv"/>
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39 <param name="reference_genome" value="reference.fasta"/>
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40 <param name="out_format" value="phylip"/>
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41 <param name="merge_alignment" value="true" />
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42
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43 <output_collection name="alignments" type="list">
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44 <element name="alignment_merged" file="expected-merged.phy"/>
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45 </output_collection>
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46 </test>
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47 <test>
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48 <param name="snv_table" value="positions.tsv"/>
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49 <param name="reference_genome" value="reference.fasta"/>
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50 <param name="out_format" value="fasta"/>
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51 <param name="merge_alignment" value="true" />
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52 <param name="keep_all" value="true" />
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53
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54 <output_collection name="alignments" type="list">
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55 <element name="alignment_merged" file="expected-merged-all.fasta"/>
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56 </output_collection>
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57 </test>
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58 <test>
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59 <param name="snv_table" value="positions.tsv"/>
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60 <param name="reference_genome" value="reference.fasta"/>
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61 <param name="out_format" value="fasta"/>
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62
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63 <output_collection name="alignments" type="list">
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64 <element name="ref1" file="ref1.fasta"/>
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65 <element name="ref2" file="ref2.fasta"/>
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66 </output_collection>
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67 </test>
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68 <test>
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69 <param name="snv_table" value="positions.tsv"/>
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70 <param name="reference_genome" value="reference.fasta"/>
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71 <param name="out_format" value="fasta"/>
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72 <param name="keep_all" value="true" />
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73
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74 <output_collection name="alignments" type="list">
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75 <element name="ref1" file="ref1-all.fasta"/>
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76 <element name="ref2" file="ref2-all.fasta"/>
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77 </output_collection>
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78 </test>
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79 </tests>
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80
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81 <help>
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82 What it does
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83 ============
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84
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85 Creates a SNV and non-variant alignment from the SNVPhyl SNV positions table and a reference genome.
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86
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87 </help>
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88
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89 <citations>
bf542eece94a "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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90 </citations>
bf542eece94a "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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parents:
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91 </tool>