Mercurial > repos > nml > vcf2snvalignment
annotate vcf2snvalignment.xml @ 0:7d66bf698382 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author | nml |
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date | Tue, 27 Aug 2019 12:33:24 -0400 |
parents | |
children | d2096d0c149e |
rev | line source |
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0
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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1 <tool id="vcf2snvalignment" name="VCF 2 snvalignment" version ="1.8.2"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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2 <description>create a snv alignment from multiple merged VCF files</description> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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3 <requirements> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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5 </requirements> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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6 <command detect_errors="exit_code"><![CDATA[ |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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7 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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8 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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9 #for $f in $vcf_collection.keys# |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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10 #set $name = str($vcf_collection[$f]).split('/')[-1] |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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11 ln -f -s '$vcf_collection[$f]' && |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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12 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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13 #if $vcf_collection[$f].metadata.bcf_index: |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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14 ln -s '${$vcf_collection[$f].metadata.bcf_index}' ${name}.csi && |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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15 #else |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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16 bcftools index $name && |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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17 #end if |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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18 #end for# |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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19 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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20 vcf2snv_alignment.pl |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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21 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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22 -r "$reference" |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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23 #if str($invalid) != 'None': |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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24 --invalid-pos "$invalid" |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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25 #end if |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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26 -f fasta |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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27 -f phylip |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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28 --numcpus \${GALAXY_SLOTS:-2} |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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29 --fasta "$ref_fasta" |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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30 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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31 #for $f in $vcf_collection.keys# |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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32 #set $path = str($vcf_collection[$f]).split('/')[-1] |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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33 --consolidate_vcf "$f=$path" |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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34 #end for# |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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35 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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36 #if $strain_list.select_list == "include": |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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37 --include '$strain_list.include' |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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38 #elif $strain_list.select_list == "exclude": |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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39 --exclude '$strain_list.exclude' |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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40 #end if |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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41 |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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42 ##mark where the output files will be sent to, simply have to match them up later in the xml output section |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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43 -o 'snvalign' |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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44 ]]> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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45 </command> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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46 <inputs> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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47 <param name="reference" type="text" label="Reference Name" value='reference' /> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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48 <param name="ref_fasta" type="data" label="Reference Fasta File" format="fasta"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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49 <param name="invalid" type="data" label="Invalid position file" format="gff,bed" optional="true"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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50 <conditional name="strain_list"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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51 <param name="select_list" type="select" label="Strain Selecting options"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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52 <option value="all">Use all strains in collection</option> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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53 <option value="include">Provide list of subset of strains to only include</option> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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54 <option value="exclude">Provide list of subset of strains to exclude</option> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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55 </param> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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56 <when value="include"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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57 <param name="include" type="data" label="List of strains to be include" format="text" optional="false"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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58 </when> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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59 <when value="exclude"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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60 <param name="exclude" type="data" label="List of strains to be excluded" format="text" optional="false"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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61 </when> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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62 <when value="all"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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63 </conditional> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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64 <param name="vcf_collection" type="data_collection" label="Combined VCF Files" help="" optional="false" format="bcf,bcf_bgzip" collection_type="list" /> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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65 </inputs> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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66 <outputs> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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67 <data format="tabular" name="positions" from_work_dir="snvalign-positions.tsv" /> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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68 <data format="fasta" name="fasta" from_work_dir="snvalign.fasta"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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69 <data format="phylip" name="phylip" from_work_dir="snvalign.phy" /> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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70 <data format="tabular" name="vcf2core" from_work_dir="snvalign-stats.csv" /> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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71 </outputs> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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72 <tests> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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73 <test> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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74 <param name="reference" value="ref"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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75 <param name="ref_fasta" value="reference.fasta"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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76 <param name="vcf_collection"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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77 <collection type="list"> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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78 <element name="v1" value="consolidate_vcf/v1.bcf.gz"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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79 <element name="v2" value="consolidate_vcf/v2.bcf.gz"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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80 </collection> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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81 </param> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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82 <output name="positions" file="expected_positions.tsv"/> |
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83 <output name="fasta" file="expected_fasta.fasta"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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84 <output name="phylip" file="expected_phylip.phy"/> |
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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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85 <output name="vcf2core" file="expected_stats.csv"/> |
7d66bf698382
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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86 </test> |
7d66bf698382
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87 </tests> |
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88 |
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89 <help> |
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90 Produces an alignment of SNVs from the merged variant/non-variant calls produced from the "consolidate_vcfs" tool. |
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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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91 </help> |
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92 |
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93 <citations> |
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94 </citations> |
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95 |
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96 </tool> |