Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
annotate varscan_mpileup2snp.xml @ 1:9a39c4105901 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author | erasmus-medical-center |
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date | Wed, 15 Feb 2017 16:16:01 -0500 |
parents | 0c5cc5763091 |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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1 <?xml version="1.0" encoding="UTF-8"?> |
1
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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2 <tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file" version="2.4.2.a"> |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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3 <description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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4 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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5 <requirements> |
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9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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6 <requirement type="package" version="2.4.2">varscan</requirement> |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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7 </requirements> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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8 |
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9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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9 <version_command>varscan 2>&1 | head -n 1</version_command> |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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10 |
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9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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11 <command detect_errors="exit_code"><![CDATA[ |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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12 varscan mpileup2snp |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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13 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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14 '${mpileup_input}' |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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15 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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16 #if $extended_parameters.parameters == "extended" |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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17 --min-coverage $extended_parameters.varscan_min_coverage |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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18 --min-reads2 $extended_parameters.varscan_min_reads2 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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19 --min-avg-qual $extended_parameters.varscan_min_avg_qual |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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20 --min-var-freq $extended_parameters.varscan_min_var_freq |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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21 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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22 --p-value $extended_parameters.varscan_p_value |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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23 $extended_parameters.varscan_strand_filter |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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24 $extended_parameters.varscan_variants |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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25 #end if |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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26 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
erasmus-medical-center
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27 #if $varscan_output == "vcf" or $varscan_output.value == "vcf" |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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28 --output-vcf 1 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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29 #end if |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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30 |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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31 > '${snv_output}' |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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32 ]]></command> |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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33 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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34 <inputs> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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35 <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? --> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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36 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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37 <conditional name="extended_parameters"> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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38 <param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings."> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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39 <option value="default">Default settings</option> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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40 <option value="extended">Extended settings</option> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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41 </param> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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42 <when value="default"> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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43 </when> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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44 <when value="extended"> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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45 <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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46 <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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47 <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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48 <param type="float" name="varscan_min_var_freq" value="0.01" label="VarScan: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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49 <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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50 <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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51 <param type="boolean" name="varscan_strand_filter" falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true" label="VarScan: Ignore variants with >90% support on one strand [1]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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52 <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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53 </when> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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54 </conditional> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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55 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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56 <param name="varscan_output" type="select" label="Output format"> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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57 <option value="vcf">VCF</option> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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58 <option value="tabular">tabular</option> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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59 </param> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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60 </inputs> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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61 |
0c5cc5763091
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62 <outputs> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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63 <data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}"> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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64 <change_format> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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65 <when input="varscan_output" value="vcf" format="vcf" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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66 </change_format> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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67 </data> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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68 </outputs> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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69 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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70 <tests> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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71 <test> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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72 <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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73 <param name="parameters" value="default" /> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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74 <param name="varscan_output_vcf" value="1" /> |
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75 |
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76 <output name="snv_output" file="hg19_mutant.vcf" /> |
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77 </test> |
1
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78 <test> |
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79 <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" /> |
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80 <param name="parameters" value="extended" /> |
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81 |
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82 <param name="varscan_min_coverage" value="8" /> |
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83 <param name="varscan_min_reads2" value="2" /> |
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84 <param name="varscan_min_avg_qual" value="15" /> |
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85 <param name="varscan_min_var_freq" value="0.01" /> |
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86 <param name="varscan_min_freq_for_hom" value="0.75" /> |
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87 <param name="varscan_p_value" value="0.99" /> |
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88 <param name="varscan_strand_filter" value=" --strand_filter 1" /> |
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89 <param name="varscan_variants" value=" --variants 0" /> |
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90 |
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91 <param name="varscan_output_vcf" value="1" /> |
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92 |
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93 <output name="snv_output" file="hg19_mutant.2.vcf" /> |
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94 </test> |
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95 </tests> |
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96 |
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97 <help> |
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98 **VarScan 2.4.2** |
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99 |
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100 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. |
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101 http://dx.doi.org/10.1101/gr.129684.111 |
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102 http://www.ncbi.nlm.nih.gov/pubmed/19542151 |
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103 |
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104 *VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. |
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105 The samtools package is not able to parallelize the mpileup generation which make it a very slow process. |
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106 Other people were aware of this and have written a version that can do parallelization: |
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107 https://github.com/mydatascience/parallel-mpileup |
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108 |
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109 .. _VarScan: http://varscan.sourceforge.net/ |
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110 |
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111 **Input formats** |
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112 |
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113 VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. |
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114 |
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115 </help> |
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116 <citations> |
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117 <citation type="doi">10.1101/gr.129684.111</citation> |
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118 </citations> |
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119 </tool> |