/tools/samtools/pileup_interval.xml
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1<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.0"> 2 <description>condenses pileup format into ranges of bases</description> 3 <requirements> 4 <requirement type="package">samtools</requirement> 5 </requirements> 6 <command interpreter="python"> 7 pileup_interval.py 8 --input=$input 9 --output=$output 10 --coverage=$coverage 11 --format=$format_type.format 12 #if $format_type.format == "ten": 13 --base=$format_type.which_base 14 --seq_column="None" 15 --loc_column="None" 16 --base_column="None" 17 --cvrg_column="None" 18 #elif $format_type.format == "manual": 19 --base="None" 20 --seq_column=$format_type.seq_column 21 --loc_column=$format_type.loc_column 22 --base_column=$format_type.base_column 23 --cvrg_column=$format_type.cvrg_column 24 #else: 25 --base="None" 26 --seq_column="None" 27 --loc_column="None" 28 --base_column="None" 29 --cvrg_column="None" 30 #end if 31 </command> 32 <inputs> 33 <param name="input" type="data" format="tabular" label="Choose a pileup file to condense:" /> 34 <conditional name="format_type"> 35 <param name="format" type="select" label="which contains:" help="See "Types of pileup datasets" below for examples"> 36 <option value="six" selected="true">Pileup with six columns (simple)</option> 37 <option value="ten">Pileup with ten columns (with consensus)</option> 38 <option value="manual">Set columns manually</option> 39 </param> 40 <when value="six" /> 41 <when value="ten"> 42 <param name="which_base" type="select" label="Which base do you want to concatenate"> 43 <option value="first" selected="true">Reference base (first)</option> 44 <option value="second">Consensus base (second)</option> 45 </param> 46 </when> 47 <when value="manual"> 48 <param name="seq_column" label="Select column with sequence name" type="data_column" numerical="false" data_ref="input" /> 49 <param name="loc_column" label="Select column with base location" type="data_column" numerical="false" data_ref="input" /> 50 <param name="base_column" label="Select column with base to concatenate" type="data_column" numerical="false" data_ref="input" /> 51 <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" /> 52 </when> 53 </conditional> 54 <param name="coverage" type="integer" value="3" label="Do not report bases with coverage less than:" /> 55 </inputs> 56 <outputs> 57 <data format="tabular" name="output" /> 58 </outputs> 59 <tests> 60 <test> 61 <param name="input" value="pileup_interval_in1.tabular" /> 62 <param name="format" value="six" /> 63 <param name="coverage" value="3" /> 64 <output name="output" file="pileup_interval_out1.tabular" /> 65 </test> 66 <test> 67 <param name="input" value="pileup_interval_in2.tabular" /> 68 <param name="format" value="ten" /> 69 <param name="which_base" value="first" /> 70 <param name="coverage" value="3" /> 71 <output name="output" file="pileup_interval_out2.tabular" /> 72 </test> 73 <test> 74 <param name="input" value="pileup_interval_in2.tabular" /> 75 <param name="format" value="manual" /> 76 <param name="seq_column" value="1" /> 77 <param name="loc_column" value="2" /> 78 <param name="base_column" value="3" /> 79 <param name="cvrg_column" value="8" /> 80 <param name="coverage" value="3" /> 81 <output name="output" file="pileup_interval_out2.tabular" /> 82 </test> 83 </tests> 84 <help> 85 86**What is does** 87 88Reduces the size of a results set by taking a pileup file and producing a condensed version showing consecutive sequences of bases meeting coverage criteria. The tool works on six and ten column pileup formats produced with *samtools pileup* command. You also can specify columns for the input file manually. The tool assumes that the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually). 89 90-------- 91 92**Types of pileup datasets** 93 94The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. 95 96.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml 97 98**Six column pileup**:: 99 100 1 2 3 4 5 6 101 --------------------------------- 102 chrM 412 A 2 ., II 103 chrM 413 G 4 ..t, IIIH 104 chrM 414 C 4 ...a III2 105 chrM 415 C 4 TTTt III7 106 107where:: 108 109 Column Definition 110 ------ ---------------------------- 111 1 Chromosome 112 2 Position (1-based) 113 3 Reference base at that position 114 4 Coverage (# reads aligning over that position) 115 5 Bases within reads where (see Galaxy wiki for more info) 116 6 Quality values (phred33 scale, see Galaxy wiki for more) 117 118**Ten column pileup** 119 120The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: 121 122 123 1 2 3 4 5 6 7 8 9 10 124 ------------------------------------------------ 125 chrM 412 A A 75 0 25 2 ., II 126 chrM 413 G G 72 0 25 4 ..t, IIIH 127 chrM 414 C C 75 0 25 4 ...a III2 128 chrM 415 C T 75 75 25 4 TTTt III7 129 130where:: 131 132 Column Definition 133 ------- ---------------------------- 134 1 Chromosome 135 2 Position (1-based) 136 3 Reference base at that position 137 4 Consensus bases 138 5 Consensus quality 139 6 SNP quality 140 7 Maximum mapping quality 141 8 Coverage (# reads aligning over that position) 142 9 Bases within reads where (see Galaxy wiki for more info) 143 10 Quality values (phred33 scale, see Galaxy wiki for more) 144 145 146.. __: http://samtools.sourceforge.net/cns0.shtml 147 148------ 149 150**The output format** 151 152The output file condenses the information in the pileup file so that consecutive bases are listed together as sequences. The starting and ending points of the sequence range are listed, with the starting value converted to a 0-based value. 153 154Given the following input with minimum coverage set to 3:: 155 156 1 2 3 4 5 6 157 --------------------------------- 158 chr1 112 G 3 ..Ta III6 159 chr1 113 T 2 aT.. III5 160 chr1 114 A 5 ,,.. IIH2 161 chr1 115 C 4 ,., III 162 chrM 412 A 2 ., II 163 chrM 413 G 4 ..t, IIIH 164 chrM 414 C 4 ...a III2 165 chrM 415 C 4 TTTt III7 166 chrM 490 T 3 a I 167 168the following would be the output:: 169 170 1 2 3 4 171 ------------------- 172 chr1 111 112 G 173 chr1 113 115 AC 174 chrM 412 415 GCC 175 chrM 489 490 T 176 177where:: 178 179 Column Definition 180 ------- ---------------------------- 181 1 Chromosome 182 2 Starting position (0-based) 183 3 Ending position (1-based) 184 4 Sequence of bases 185 186 </help> 187</tool> 188 189