Mercurial > repos > devteam > varscan_version_2
annotate varscan_mpileup.xml @ 5:6e4920c4285f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
| author | devteam |
|---|---|
| date | Fri, 03 Feb 2017 08:25:53 -0500 |
| parents | 24670f9f6839 |
| children |
| rev | line source |
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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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1 <tool id="varscan" name="VarScan" version="2.4.2"> |
| 2 | 2 <description>for variant detection</description> |
| 3 | |
| 4 <requirements> | |
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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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5 <requirement type="package" version="2.4.2">varscan</requirement> |
| 2 | 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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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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13 <version_command><![CDATA[ |
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6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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14 varscan 2>&1 | head -n 1 |
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6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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15 ]]></version_command> |
| 2 | 16 |
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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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17 <command><![CDATA[ |
| 2 | 18 ## Set up samples list file. |
| 19 #if $sample_names.strip() != '': | |
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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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20 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt && |
| 2 | 21 #end if |
| 22 | |
| 23 ## Set up command + input. | |
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5
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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24 varscan ${cmd} ${input} |
| 2 | 25 --min-coverage ${min_coverage} |
| 26 --min-reads2 ${min_supporting_reads} | |
| 27 --min-avg-qual ${min_avg_qual} | |
| 28 --min-var-freq ${min_var_freq} | |
| 29 --min-freq-for-hom ${min_freq_for_hom} | |
| 30 --p-value ${p_value} | |
| 31 #if str($strand_filter) == 'yes': | |
| 32 --strand-filter 1 | |
| 33 #end if | |
| 34 | |
| 35 ## Report only variants in consensus. | |
| 36 #if str($cmd) == 'mpileup2cns': | |
| 37 --variants | |
| 38 #end if | |
| 39 | |
| 40 ## Set up outputs. | |
| 41 --output-vcf 1 > $output | |
| 42 | |
| 43 #if $sample_names.strip() != '': | |
| 44 --vcf-sample-list samples_list.txt | |
| 45 #end if | |
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5
6e4920c4285f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
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changeset
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46 ]]></command> |
| 2 | 47 |
| 48 <inputs> | |
| 49 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/> | |
| 50 | |
| 51 <param name="cmd" type="select" label="Analysis type"> | |
| 52 <option value="mpileup2snp" selected="True">single nucleotide variation</option> | |
| 53 <option value="mpileup2indel">insertions and deletions</option> | |
| 54 <option value="mpileup2cns">consensus genotype</option> | |
| 55 </param> | |
| 56 | |
| 57 <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"/> | |
| 58 <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"/> | |
| 59 <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/> | |
| 60 <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/> | |
| 61 <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/> | |
| 62 <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/> | |
| 63 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand"> | |
| 64 <option value="no" selected="True">no</option> | |
| 65 <option value="yes">yes</option> | |
| 66 </param> | |
| 67 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> | |
| 68 </inputs> | |
| 69 | |
| 70 <outputs> | |
| 71 <data name="output" format="vcf"/> | |
| 72 </outputs> | |
| 73 <tests> | |
| 74 <test> | |
| 75 <param name="input" value="test_in1.pileup" /> | |
| 76 <param name="cmd" value="mpileup2cns" /> | |
| 77 <param name="min_coverage" value="8" /> | |
| 78 <param name="min_supporting_reads" value="2" /> | |
| 79 <param name="min_avg_qual" value="15" /> | |
| 80 <param name="min_var_freq" value="0.01" /> | |
| 81 <param name="min_freq_for_hom" value="0.75" /> | |
| 82 <param name="p_value" value="0.99" /> | |
| 83 <param name="strand_filter" value="no" /> | |
| 84 <param name="sample_names" value="" /> | |
| 85 <output name="output" file="test_out1.vcf" lines_diff="0" /> | |
| 86 </test> | |
| 87 </tests> | |
| 88 | |
| 89 <help> | |
| 90 **VarScan Overview** | |
| 91 | |
| 92 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_. | |
| 93 | |
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4
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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94 .. _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
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parents:
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changeset
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95 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html |
| 2 | 96 |
| 97 **Input** | |
| 98 | |
| 99 :: | |
| 100 | |
| 101 mpileup file - The SAMtools mpileup file | |
| 102 | |
| 103 | |
| 104 **Output** | |
| 105 | |
| 106 VarScan produces a VCF 4.1 dataset as output. | |
| 107 | |
| 108 **Parameters** | |
| 109 | |
| 110 :: | |
| 111 | |
| 112 analysis type | |
| 113 single nucleotide detection Identify SNPs from an mpileup file | |
| 114 insertions and deletion Identify indels an mpileup file | |
| 115 consensus genotype Call consensus and variants from an mpileup file | |
| 116 | |
| 117 min-coverage | |
| 118 Minimum read depth at a position to make a call [8] | |
| 119 | |
| 120 min-reads2 | |
| 121 Minimum supporting reads at a position to call variants [2] | |
| 122 | |
| 123 min-avg-qual | |
| 124 Minimum base quality at a position to count a read [15] | |
| 125 | |
| 126 min-var-freq | |
| 127 Minimum variant allele frequency threshold [0.01] | |
| 128 | |
| 129 min-freq-for-hom | |
| 130 Minimum frequency to call homozygote [0.75] | |
| 131 | |
| 132 p-value | |
| 133 Default p-value threshold for calling variants [99e-02] | |
| 134 | |
| 135 strand-filter | |
| 136 Ignore variants with >90% support on one strand [1] | |
| 137 | |
| 138 output-vcf | |
| 139 If set to 1, outputs in VCF format | |
| 140 | |
| 141 vcf-sample-list | |
| 142 For VCF output, a list of sample names in order, one per line | |
| 143 | |
| 144 variants | |
| 145 Report only variant (SNP/indel) positions [0] | |
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4
24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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146 </help> |
| 2 | 147 |
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4
24670f9f6839
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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148 <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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149 <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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150 </citations> |
| 2 | 151 </tool> |