Mercurial > repos > nml > positions2snv_alignment

annotate positions2snv_alignment.xml @ 0:e2cec726fa79 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 12:32:15 -0400
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children 1cf81ca17e9d
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e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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1 <tool id="positions2snv_alignment" name="Positions to SNV alignment" version ="1.8.2">
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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2 <description>Create a SNV-only alignment from the SNVPhyl positions table.</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_alignment.pl -i $snv_table -o $output -f $out_format $keep_all
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8 #if $reference_name:
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9 --reference-name $reference_name
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10 #end if
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11 ]]></command>
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12 <inputs>
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13 <param name="snv_table" type="data" label="SNV table" format="tabular"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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14 <param name="out_format" type="select" label="Output alignment format">
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15 <option value="phylip">Phylip alignment format</option>
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16 <option value="fasta">FASTA alignment format</option>
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17 </param>
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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="" />
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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20 <param name="reference_name" type="text" label="Reference genome name" value="Reference"
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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21 help="Name of reference genome in produced alignment" />
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22 </inputs>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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23 <outputs>
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24 <data format="phylip" name="output">
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25 <change_format>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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26 <when input="out_format" value="phylip" format="phylip"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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27 <when input="out_format" value="fasta" format="fasta"/>
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28 </change_format>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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29 </data>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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30 </outputs>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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31 <tests>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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32 <test>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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33 <param name="snv_table" value="positions.tsv"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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34 <param name="out_format" value="phylip"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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35
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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36 <output name="output" file="expected.phy"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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37 </test>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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38 <test>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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39 <param name="snv_table" value="positions.tsv"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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40 <param name="out_format" value="fasta"/>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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41
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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42 <output name="output" file="expected.fasta"/>
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43 </test>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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44 <test>
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45 <param name="snv_table" value="positions.tsv"/>
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46 <param name="out_format" value="fasta"/>
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47 <param name="keep_all" value="true" />
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48
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49 <output name="output" file="expected-all.fasta"/>
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50 </test>
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51 <test>
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52 <param name="snv_table" value="positions.tsv"/>
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53 <param name="out_format" value="fasta"/>
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54
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55 <output name="output" file="expected.fasta"/>
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56 </test>
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57 <test>
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58 <param name="snv_table" value="positions.tsv"/>
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59 <param name="out_format" value="fasta"/>
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60 <param name="reference_name" value="ChangedRefName" />
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61
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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62 <output name="output" file="expected-changed-ref-name.fasta"/>
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63 </test>
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64 </tests>
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65
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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66 <help>
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67 What it does
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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68 ============
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69
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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70 Creates a SNV-only alignment from the SNVPhyl SNV positions table.
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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71
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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72 </help>
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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73
e2cec726fa79 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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74 <citations>
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75 </citations>
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76 </tool>