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annotate varscan_mpileup.xml @ 4:24670f9f6839 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 12:01:23 -0500 |
| parents | 89702e7ec3c3 |
| children | 6e4920c4285f |
| rev | line source |
|---|---|
| 2 | 1 <tool id="varscan" name="Varscan" version="0.1"> |
| 2 <description>for variant detection</description> | |
| 3 | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.3.6">varscan</requirement> | |
| 6 </requirements> | |
| 7 | |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <stdio> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <regex match="Exception" source="both" level="fatal" description="Tool exception"/> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <regex match=".*" source="both" level="log" description="tool progress"/> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 </stdio> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> |
| 2 | 14 |
| 15 <command> | |
| 16 ## Set up samples list file. | |
| 17 #if $sample_names.strip() != '': | |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt; |
| 2 | 19 #end if |
| 20 | |
| 21 ## Set up command + input. | |
| 22 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input} | |
| 23 --min-coverage ${min_coverage} | |
| 24 --min-reads2 ${min_supporting_reads} | |
| 25 --min-avg-qual ${min_avg_qual} | |
| 26 --min-var-freq ${min_var_freq} | |
| 27 --min-freq-for-hom ${min_freq_for_hom} | |
| 28 --p-value ${p_value} | |
| 29 #if str($strand_filter) == 'yes': | |
| 30 --strand-filter 1 | |
| 31 #end if | |
| 32 | |
| 33 ## Report only variants in consensus. | |
| 34 #if str($cmd) == 'mpileup2cns': | |
| 35 --variants | |
| 36 #end if | |
| 37 | |
| 38 ## Set up outputs. | |
| 39 --output-vcf 1 > $output | |
| 40 | |
| 41 #if $sample_names.strip() != '': | |
| 42 --vcf-sample-list samples_list.txt | |
| 43 #end if | |
| 44 </command> | |
| 45 | |
| 46 <inputs> | |
| 47 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/> | |
| 48 | |
| 49 <param name="cmd" type="select" label="Analysis type"> | |
| 50 <option value="mpileup2snp" selected="True">single nucleotide variation</option> | |
| 51 <option value="mpileup2indel">insertions and deletions</option> | |
| 52 <option value="mpileup2cns">consensus genotype</option> | |
| 53 </param> | |
| 54 | |
| 55 <param name="min_coverage" type="integer" value="8" min="1" max="200" label="Minimum read depth" help="Minimum depth at a position to make a call"/> | |
| 56 <param name="min_supporting_reads" type="integer" value="2" min="1" max="200" label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/> | |
| 57 <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/> | |
| 58 <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/> | |
| 59 <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/> | |
| 60 <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/> | |
| 61 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand"> | |
| 62 <option value="no" selected="True">no</option> | |
| 63 <option value="yes">yes</option> | |
| 64 </param> | |
| 65 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> | |
| 66 </inputs> | |
| 67 | |
| 68 <outputs> | |
| 69 <data name="output" format="vcf"/> | |
| 70 </outputs> | |
| 71 | |
| 72 <trackster_conf> | |
| 73 </trackster_conf> | |
| 74 | |
| 75 <tests> | |
| 76 <test> | |
| 77 <param name="input" value="test_in1.pileup" /> | |
| 78 <param name="cmd" value="mpileup2cns" /> | |
| 79 <param name="min_coverage" value="8" /> | |
| 80 <param name="min_supporting_reads" value="2" /> | |
| 81 <param name="min_avg_qual" value="15" /> | |
| 82 <param name="min_var_freq" value="0.01" /> | |
| 83 <param name="min_freq_for_hom" value="0.75" /> | |
| 84 <param name="p_value" value="0.99" /> | |
| 85 <param name="strand_filter" value="no" /> | |
| 86 <param name="sample_names" value="" /> | |
| 87 <output name="output" file="test_out1.vcf" lines_diff="0" /> | |
| 88 </test> | |
| 89 </tests> | |
| 90 | |
| 91 <help> | |
| 92 **VarScan Overview** | |
| 93 | |
| 94 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_. | |
| 95 | |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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96 .. _VarScan: http://dkoboldt.github.io/varscan/ |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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diff
changeset
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97 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html |
| 2 | 98 |
| 99 **Input** | |
| 100 | |
| 101 :: | |
| 102 | |
| 103 mpileup file - The SAMtools mpileup file | |
| 104 | |
| 105 | |
| 106 **Output** | |
| 107 | |
| 108 VarScan produces a VCF 4.1 dataset as output. | |
| 109 | |
| 110 **Parameters** | |
| 111 | |
| 112 :: | |
| 113 | |
| 114 analysis type | |
| 115 single nucleotide detection Identify SNPs from an mpileup file | |
| 116 insertions and deletion Identify indels an mpileup file | |
| 117 consensus genotype Call consensus and variants from an mpileup file | |
| 118 | |
| 119 min-coverage | |
| 120 Minimum read depth at a position to make a call [8] | |
| 121 | |
| 122 min-reads2 | |
| 123 Minimum supporting reads at a position to call variants [2] | |
| 124 | |
| 125 min-avg-qual | |
| 126 Minimum base quality at a position to count a read [15] | |
| 127 | |
| 128 min-var-freq | |
| 129 Minimum variant allele frequency threshold [0.01] | |
| 130 | |
| 131 min-freq-for-hom | |
| 132 Minimum frequency to call homozygote [0.75] | |
| 133 | |
| 134 p-value | |
| 135 Default p-value threshold for calling variants [99e-02] | |
| 136 | |
| 137 strand-filter | |
| 138 Ignore variants with >90% support on one strand [1] | |
| 139 | |
| 140 output-vcf | |
| 141 If set to 1, outputs in VCF format | |
| 142 | |
| 143 vcf-sample-list | |
| 144 For VCF output, a list of sample names in order, one per line | |
| 145 | |
| 146 variants | |
| 147 Report only variant (SNP/indel) positions [0] | |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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148 </help> |
| 2 | 149 |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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150 <citations> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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151 <citation type="doi">10.1101/gr.129684.111</citation> |
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24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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152 </citations> |
| 2 | 153 </tool> |