Mercurial > repos > nml > positions2snv_alignment

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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author nml
date Tue, 23 Jun 2020 10:26:59 -0400
parents e2cec726fa79
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1cf81ca17e9d "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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1 <tool id="positions2snv_alignment" name="Positions to SNV alignment" version ="@VERSION@+galaxy1">
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2 <description>Create a SNV-only alignment from the SNVPhyl positions table.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 positions2snv_alignment.pl -i $snv_table -o $output -f $out_format $keep_all
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9 #if $reference_name:
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10 --reference-name $reference_name
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11 #end if
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12 ]]></command>
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13 <inputs>
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14 <param name="snv_table" type="data" label="SNV table" format="tabular"/>
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15 <param name="out_format" type="select" label="Output alignment format">
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16 <option value="phylip">Phylip alignment format</option>
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17 <option value="fasta">FASTA alignment format</option>
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18 </param>
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19 <param name="keep_all" type="boolean" checked="false" label="Keep all positions"
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20 help="Keep all positions with status 'filtered' in the SNV alignment" truevalue="--keep-all" falsevalue="" />
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21 <param name="reference_name" type="text" label="Reference genome name" value="Reference"
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22 help="Name of reference genome in produced alignment" />
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23 </inputs>
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24 <outputs>
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25 <data format="phylip" name="output">
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26 <change_format>
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27 <when input="out_format" value="phylip" format="phylip"/>
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28 <when input="out_format" value="fasta" format="fasta"/>
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29 </change_format>
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30 </data>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="snv_table" value="positions.tsv"/>
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35 <param name="out_format" value="phylip"/>
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36
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37 <output name="output" file="expected.phy"/>
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38 </test>
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39 <test>
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40 <param name="snv_table" value="positions.tsv"/>
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41 <param name="out_format" value="fasta"/>
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42
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43 <output name="output" file="expected.fasta"/>
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44 </test>
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45 <test>
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46 <param name="snv_table" value="positions.tsv"/>
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47 <param name="out_format" value="fasta"/>
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48 <param name="keep_all" value="true" />
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49
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50 <output name="output" file="expected-all.fasta"/>
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51 </test>
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52 <test>
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53 <param name="snv_table" value="positions.tsv"/>
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54 <param name="out_format" value="fasta"/>
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55
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56 <output name="output" file="expected.fasta"/>
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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="out_format" value="fasta"/>
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61 <param name="reference_name" value="ChangedRefName" />
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62
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63 <output name="output" file="expected-changed-ref-name.fasta"/>
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64 </test>
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65 </tests>
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66
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67 <help>
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68 What it does
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69 ============
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70
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71 Creates a SNV-only alignment from the SNVPhyl SNV positions table.
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72
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73 </help>
1
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74 <expand macro="citations"/>
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75 </tool>