Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
annotate varscan_mpileup2snp_from_bam.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"?> |
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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_from_bam" name="VarScan2 Call SNPs from BAM" 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 reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.</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
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5 <requirements> |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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6 <requirement type="package" version="2.4.2">varscan</requirement> |
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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7 <requirement type="package" version="0.6.5">sambamba</requirement> |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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8 </requirements> |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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9 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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10 <version_command>varscan 2>&1 | head -n 1</version_command> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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11 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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12 <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
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13 #for $alignment in $alignments |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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14 ln -f -s '${alignment.metadata.bam_index}' '${alignment}.bai' && |
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 #end for |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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16 |
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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17 sambamba mpileup |
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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18 -t \${GALAXY_SLOTS:-4} |
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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19 |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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20 #for $alignment in $alignments |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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21 '${alignment}' |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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22 #end for |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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23 |
1
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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24 --samtools |
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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25 -f |
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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 #if $reference_genome_source.source_select == "indexed_filtered" |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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27 '$reference_genome_source.reference_genome' |
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 #else if $reference_genome_source.source_select == "indexed_all" |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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29 '$reference_genome_source.reference_genome' |
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 #else if $reference_genome_source.source_select == "history" |
9a39c4105901
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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31 '$reference_genome_source.reference_genome' |
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 #else |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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33 <!-- |
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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34 This is a workaround to obtain the "genome.fa" file that |
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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35 corresponds to the dbkey of the alignments. |
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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36 Because this file is "calculated" during run-time, it can |
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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37 be used in a workflow. |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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38 --> |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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39 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-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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40 #end if |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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41 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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42 #if $extended_parameters_regions.sambamba_regions == "region" |
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43 -r '${extended_parameters_regions.sambamba_r}' |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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44 #elif $extended_parameters_regions.sambamba_regions == "regions_file_pos" or $extended_parameters_regions.sambamba_regions == "regions_file_bed" |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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45 -l '${extended_parameters_regions.sambamba_l}' |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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46 #end if |
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47 |
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48 #if $extended_parameters.parameters == "extended" |
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49 $extended_parameters.sambamba_6 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
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50 $extended_parameters.sambamba_A |
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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51 $extended_parameters.sambamba_B |
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52 -C $extended_parameters.sambamba_C |
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53 -d $extended_parameters.sambamba_d |
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54 $extended_parameters.sambamba_E |
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55 -M $extended_parameters.sambamba_M |
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56 $extended_parameters.sambamba_R |
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57 -q $extended_parameters.sambamba_q |
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58 -Q $extended_parameters.sambamba_Q |
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59 |
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60 -e $extended_parameters.sambamba_e |
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61 -F $extended_parameters.sambamba_F |
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62 -h $extended_parameters.sambamba_h |
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63 $extended_parameters.sambamba_I |
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64 -L $extended_parameters.sambamba_L |
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65 -m $extended_parameters.sambamba_m |
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66 -o $extended_parameters.sambamba_o |
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67 $extended_parameters.sambamba_p |
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68 -P $extended_parameters.sambamba_P |
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69 #end if |
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70 | varscan mpileup2snp |
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71 |
1
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72 #if $extended_parameters.parameters == "extended" |
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73 --min-coverage $extended_parameters.varscan_min_coverage |
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74 --min-reads2 $extended_parameters.varscan_min_reads2 |
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75 --min-avg-qual $extended_parameters.varscan_min_avg_qual |
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76 --min-var-freq $extended_parameters.varscan_min_var_freq |
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77 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom |
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78 --p-value $extended_parameters.varscan_p_value |
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79 $extended_parameters.varscan_strand_filter |
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80 $extended_parameters.varscan_variants |
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81 #end if |
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82 |
1
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83 #if $varscan_output == "vcf" or $varscan_output.value == "vcf" |
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84 --output-vcf 1 |
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85 #end if |
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86 |
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87 > '$snv_output' |
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88 ]]></command> |
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89 |
0
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90 <inputs> |
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91 <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file(s)" help="Mapped reads in BAM or SAM format."/> |
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92 |
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93 <!-- Find out how to access the reference genome from the BAM file(s) --> |
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94 <conditional name="reference_genome_source"> |
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95 <param name="source_select" type="select" label="Fasta Source"> |
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96 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> |
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97 <option value="history">Use reference from the history</option> |
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98 <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> |
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99 <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> |
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100 </param> |
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101 <when value="history"> |
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102 <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> |
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103 </when> |
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104 <when value="indexed_filtered"> |
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105 <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > |
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106 <options from_data_table="all_fasta"> |
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107 <column name="name" index="2"/> |
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108 <column name="dbkey" index="1"/> |
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109 <column name="value" index="3"/><!-- Value is the path of the fasta file --> |
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110 <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" /> |
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111 <validator type="no_options" message="No indexes are available for the selected input dataset" /> |
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112 </options> |
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113 </param> |
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114 </when> |
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115 <when value="indexed_all"> |
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116 <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > |
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117 <options from_data_table="all_fasta"> |
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118 <column name="name" index="2"/> |
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119 <column name="dbkey" index="1"/> |
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120 <column name="value" index="3"/><!-- Value is the path of the fasta file --> |
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121 <validator type="no_options" message="No indexes are available for the selected input dataset" /> |
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122 </options> |
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123 </param> |
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124 </when> |
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125 <when value="attribute" /> |
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126 </conditional> |
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127 |
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128 <conditional name="extended_parameters_regions"> |
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129 <param name="sambamba_regions" type="select" label="Region specific parameters" help="Let sambamba target specific genomic locations."> |
0
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130 <option value="entire_genome">Entire genome</option> |
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131 <option value="region">Specific region</option> |
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132 <option value="regions_file_pos">Specific positions (file); list of positions</option> |
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133 <option value="regions_file_bed">Specific regions (file); list of regions in BED</option> |
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134 </param> |
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135 <when value="entire_genome" /> |
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136 <when value="region"> |
1
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137 <param type="text" name="sambamba_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" /> |
0
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138 </when> |
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139 <when value="regions_file_pos"> |
1
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140 <param type="data" name="sambamba_l" format="tabular" label="Samtools: list of positions (chr pos)" /> |
0
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141 </when> |
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142 <when value="regions_file_bed"> |
1
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143 <param type="data" name="sambamba_l" format="bed" label="Samtools: specific regions (BED)" /> |
0
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144 </when> |
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145 </conditional> |
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146 |
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147 <conditional name="extended_parameters"> |
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148 <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and sambamba settings."> |
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149 <option value="default">Default settings</option> |
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150 <option value="extended">Extended settings</option> |
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151 </param> |
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152 <when value="default" /> |
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153 <when value="extended"> |
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154 <param type="boolean" name="sambamba_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" /> |
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155 <param type="boolean" name="sambamba_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" /> |
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156 <param type="boolean" name="sambamba_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" /> |
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157 <param type="integer" name="sambamba_C" value="0" label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" /> |
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158 <param type="integer" name="sambamba_d" value="250" label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" /> |
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159 <param type="boolean" name="sambamba_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" /> |
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160 <param type="integer" name="sambamba_M" value="60" label="cap mapping quality at INT [60]" /> |
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161 <param type="boolean" name="sambamba_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" /> |
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162 <param type="integer" name="sambamba_q" value="0" label="Samtools: skip alignments with mapQ smaller than INT [0]" /> |
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163 <param type="integer" name="sambamba_Q" value="13" label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" /> |
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164 |
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165 <param type="integer" name="sambamba_e" value="20" label="Samtools: Phred-scaled gap extension seq error probability [20]" /> |
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166 <param type="float" name="sambamba_F" value="0.002" label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> |
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167 <param type="integer" name="sambamba_h" value="100" label="Samtools: coefficient for homopolymer errors [100]" /> |
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168 <param type="boolean" name="sambamba_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" /> |
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169 <param type="integer" name="sambamba_L" value="250" label="Samtools: max per-sample depth for INDEL calling [250]" /> |
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170 <param type="integer" name="sambamba_m" value="1" label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" /> |
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171 <param type="integer" name="sambamba_o" value="40" label="Samtools: Phred-scaled gap open sequencing error probability [40]" /> |
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172 <param type="boolean" name="sambamba_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" /> |
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173 <param type="text" name="sambamba_P" value="all" label="Samtools: comma separated list of platforms for indels [all]" /> |
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174 |
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175 <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" /> |
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176 <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" /> |
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177 <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" /> |
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178 <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" /> |
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179 <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" /> |
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180 <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" /> |
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181 <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]" /> |
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182 <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" /> |
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183 </when> |
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184 </conditional> |
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185 |
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186 <param name="varscan_output" type="select" label="Output format"> |
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187 <option value="vcf">VCF</option> |
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188 <option value="tabular">tabular</option> |
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189 </param> |
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190 </inputs> |
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191 |
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192 <outputs> |
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193 <data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}"> |
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194 <change_format> |
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195 <when input="varscan_output" value="vcf" format="vcf" /> |
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196 </change_format> |
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197 </data> |
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198 </outputs> |
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199 |
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200 <tests> |
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201 <test><!-- Use classical sambamba --> |
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202 <param name="alignments" value="example.bam" ftype="bam" /> |
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203 |
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204 <param name="source_select" value="history" /> |
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205 <param name="reference_genome" value="example.fa" /> |
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206 |
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207 <param name="sambamba_regions" value="entire_genome" /> |
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208 |
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209 <param name="parameters" value="default" /> |
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210 <param name="varscan_output_vcf" value="1" /> |
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211 |
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212 |
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213 <output name="snv_output" file="example.vcf" /> |
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214 </test> |
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215 </tests> |
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216 |
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217 <help> |
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218 **VarScan 2.4.2** |
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219 |
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220 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. |
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221 http://dx.doi.org/10.1101/gr.129684.111 |
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222 http://www.ncbi.nlm.nih.gov/pubmed/19542151 |
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223 |
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224 *VarScan* requires mpileup input files, generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing can be by-passed using this tool. |
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225 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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226 |
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227 .. _VarScan: http://varscan.sourceforge.net/ |
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228 |
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229 **Input formats** |
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230 |
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231 VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). |
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232 The alignment files must have a reference genome (dbkey) in Galaxy. |
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233 |
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234 Contact |
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235 ------- |
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236 |
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237 The tool wrapper has been written by Youri Hoogstrate from the Erasmus |
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238 Medical Center (Rotterdam, Netherlands) |
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239 </help> |
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240 <citations> |
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241 <citation type="doi">10.1101/gr.129684.111</citation> |
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242 </citations> |
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243 </tool> |