Mercurial > repos > nml > consolidate_vcfs
annotate consolidate_vcfs.xml @ 1:4c249c0aebad draft default tip
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author | nml |
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date | Tue, 23 Jun 2020 10:25:20 -0400 |
parents | b42c82186e85 |
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rev | line source |
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1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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1 <tool id="consolidate_vcfs" name="Consolidate VCFs" version ="@VERSION@+galaxy1"> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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2 <description>combine freebayes and mpileup files for use by vcf2snvalignment</description> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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3 <macros> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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4 <import>macros.xml</import> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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5 </macros> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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6 <expand macro="requirements"/> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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7 <command detect_errors="exit_code"><![CDATA[ |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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8 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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9 #set $name = str($freebayes).split('/')[-1] |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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10 ln -f -s $freebayes && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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11 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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12 #if $freebayes.metadata.bcf_index: |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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13 ln -s '${$freebayes.metadata.bcf_index}' ${name}.csi && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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14 #else |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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15 bcftools index $name && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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16 #end if |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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17 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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18 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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19 #set $name = str($mpileup).split('/')[-1] |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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20 ln -f -s $mpileup && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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21 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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22 #if $mpileup.metadata.bcf_index: |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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23 ln -s '${$mpileup.metadata.bcf_index}' ${name}.csi && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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24 #else |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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25 bcftools index $name && |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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26 #end if |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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27 |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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28 ## If there is no density filtering performed we still need to output an empty file |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
parents:
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29 #if not $use_density_filter: |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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30 echo '#No density filtering' > '$filtered_density' && |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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31 #end if |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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32 |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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33 consolidate_vcfs.pl |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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34 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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35 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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36 -c "$coverage" |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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37 --min-mean-mapping "$mean_mapping" |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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38 --snv-abundance-ratio "$snv_abundance_ratio" |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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39 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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40 #set $path = str($freebayes).split('/')[-1] |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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41 --vcfsplit "$path" |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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42 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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43 #set $path = str($mpileup).split('/')[-1] |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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44 --mpileup "$path" |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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45 |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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46 #if not $use_density_filter: |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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47 --skip-density-filter |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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48 #else |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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49 #if $filtered_density: |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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50 --filtered-density-out '$filtered_density' |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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51 #end if |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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52 |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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53 #if $window_size: |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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54 --window-size "$window_size" |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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55 #end if |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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56 #if $threshold: |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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57 --density-threshold "$threshold" |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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58 #end if |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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59 #end if |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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60 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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61 ##mark where the output files will be sent to, simply have to match them up later in the xml output section |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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62 -o $bcf_combined |
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4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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63 |
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b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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64 ]]> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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65 </command> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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66 <inputs> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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67 <param name="coverage" type="integer" value="15" label="Minimum coverage" help="(--coverage-cutoff)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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68 <param name="mean_mapping" type="integer" value="30" label="Minimum mean mapping quality" help="(--min-mean-mapping)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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69 <param name="snv_abundance_ratio" type="text" value="0.75" optional="false" label="SNV abundance ratio" help="(--snv-abundance-ratio)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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70 <param name="freebayes" type="data" label="FreeBayes filtered BCF" optional="false" format="bcf_bgzip,bcf" help="(--vcfsplit)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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71 <param name="mpileup" type="data" label="Mpileup BCF" optional="false" format="bcf_bgzip,bcf" help="(--mpileup)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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72 <param name="use_density_filter" type="boolean" checked="true" label="Apply SNV density filtering" help="(--skip-density-filter)" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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73 <param name="window_size" type="integer" min="1" label="SNV Density Filtering: Size of search window" format="" optional="false" value="500" |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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74 help="(--window-size) Size of the search window used to find high-density SNV regions. Only valid if density filtering is enabled." /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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75 <param name="threshold" type="integer" min="1" label="SNV Density Filtering: Density threshold cutoff" format="" optional="false" value="2" |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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76 help="(--density-threshold) The SNV threshold within a window to determine of this is a high-density SNV region. Only valid if density filtering is enabled." /> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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77 </inputs> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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78 <outputs> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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79 <data format="bcf_bgzip" name="bcf_combined"/> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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80 <data format="txt" name="filtered_density" label="High density regions"/> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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81 </outputs> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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82 <tests> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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83 <test> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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|
84 <param name="coverage" value="5"/> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
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|
85 <param name="freebayes" value="freebayes/v1.bcf" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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86 <param name="mpileup" value="mpileup/v1.bcf" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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87 <param name="mean_mapping" value="30" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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88 <param name="snv_abundance_ratio" value="0.75" /> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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89 <param name="use_density_filter" value="true" /> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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90 <param name="window_size" value="500" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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91 <param name="threshold" value="2" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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92 <output name="bcf_combined" file="v1.bcf.gz" compare="sim_size" delta="500"/> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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93 <output name="filtered_density" file="expected_regions_empty.txt"/> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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94 </test> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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95 <test> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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96 <param name="coverage" value="5"/> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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97 <param name="freebayes" value="freebayes/v2.bcf" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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98 <param name="mpileup" value="mpileup/v2.bcf" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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99 <param name="mean_mapping" value="30" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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100 <param name="snv_abundance_ratio" value="0.75" /> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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101 <param name="use_density_filter" value="true" /> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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102 <param name="window_size" value="500" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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103 <param name="threshold" value="2" /> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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104 <output name="bcf_combined" file="v2.bcf.gz" compare="sim_size" delta="500"/> |
1
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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105 <output name="filtered_density" file="expected_regions_empty.txt"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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106 </test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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107 <test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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108 <param name="coverage" value="5"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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109 <param name="freebayes" value="freebayes/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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110 <param name="mpileup" value="mpileup/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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111 <param name="mean_mapping" value="30" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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112 <param name="snv_abundance_ratio" value="0.75" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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113 <param name="use_density_filter" value="true" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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114 <param name="window_size" value="10" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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115 <param name="threshold" value="3" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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116 <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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117 <output name="filtered_density" file="expected_regions_v3.txt"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
118 </test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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119 <test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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120 <param name="coverage" value="5"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
parents:
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121 <param name="freebayes" value="freebayes/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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122 <param name="mpileup" value="mpileup/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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123 <param name="mean_mapping" value="30" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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124 <param name="snv_abundance_ratio" value="0.75" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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125 <param name="use_density_filter" value="true" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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126 <param name="window_size" value="10" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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127 <param name="threshold" value="4" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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128 <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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129 <output name="filtered_density" file="expected_regions_empty.txt"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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130 </test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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131 <test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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132 <param name="coverage" value="5"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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133 <param name="freebayes" value="freebayes/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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134 <param name="mpileup" value="mpileup/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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135 <param name="mean_mapping" value="30" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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136 <param name="snv_abundance_ratio" value="0.75" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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137 <param name="window_size" value="1" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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138 <param name="threshold" value="2" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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139 <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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140 <output name="filtered_density" file="expected_regions_empty.txt"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
141 </test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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142 <test> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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143 <param name="coverage" value="5"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
parents:
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|
144 <param name="freebayes" value="freebayes/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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145 <param name="mpileup" value="mpileup/v3.bcf" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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146 <param name="mean_mapping" value="30" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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147 <param name="snv_abundance_ratio" value="0.75" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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148 <param name="use_density_filter" value="false" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
149 <param name="window_size" value="10" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
150 <param name="threshold" value="3" /> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
151 <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> |
4c249c0aebad
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
nml
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|
152 <output name="filtered_density" file="expected_regions_disabled.txt"/> |
0
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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153 </test> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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154 </tests> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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|
155 |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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|
156 <help> |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
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|
157 Merges variant and non-variant calls (in VCF format) produced from two independent base callers, FreeBayes, and SAMtools/BCFtools. Produces a merged set of high-quality variant and non-variant calls (in BCF format). Optionally, produces a list of SNV-dense regions above the passed thresholds. |
b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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158 </help> |
1
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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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159 <expand macro="citations"/> |
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b42c82186e85
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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160 </tool> |