Mercurial > repos > devteam > pileup_interval
annotate pileup_interval.xml @ 2:1e897622570e draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:28:06 -0400 |
| parents | 36826b2b4096 |
| children | d78f28cae91b |
| rev | line source |
|---|---|
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1e897622570e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.2"> |
| 0 | 2 <description>condenses pileup format into ranges of bases</description> |
| 3 <command interpreter="python"> | |
| 4 pileup_interval.py | |
| 5 --input=$input | |
| 6 --output=$output | |
| 7 --coverage=$coverage | |
| 8 --format=$format_type.format | |
| 9 #if $format_type.format == "ten": | |
| 10 --base=$format_type.which_base | |
| 11 --seq_column="None" | |
| 12 --loc_column="None" | |
| 13 --base_column="None" | |
| 14 --cvrg_column="None" | |
| 15 #elif $format_type.format == "manual": | |
| 16 --base="None" | |
| 17 --seq_column=$format_type.seq_column | |
| 18 --loc_column=$format_type.loc_column | |
| 19 --base_column=$format_type.base_column | |
| 20 --cvrg_column=$format_type.cvrg_column | |
| 21 #else: | |
| 22 --base="None" | |
| 23 --seq_column="None" | |
| 24 --loc_column="None" | |
| 25 --base_column="None" | |
| 26 --cvrg_column="None" | |
| 27 #end if | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <param name="input" type="data" format="tabular" label="Choose a pileup file to condense:" /> | |
| 31 <conditional name="format_type"> | |
| 32 <param name="format" type="select" label="which contains:" help="See "Types of pileup datasets" below for examples"> | |
| 33 <option value="six" selected="true">Pileup with six columns (simple)</option> | |
| 34 <option value="ten">Pileup with ten columns (with consensus)</option> | |
| 35 <option value="manual">Set columns manually</option> | |
| 36 </param> | |
| 37 <when value="six" /> | |
| 38 <when value="ten"> | |
| 39 <param name="which_base" type="select" label="Which base do you want to concatenate"> | |
| 40 <option value="first" selected="true">Reference base (first)</option> | |
| 41 <option value="second">Consensus base (second)</option> | |
| 42 </param> | |
| 43 </when> | |
| 44 <when value="manual"> | |
| 45 <param name="seq_column" label="Select column with sequence name" type="data_column" numerical="false" data_ref="input" /> | |
| 46 <param name="loc_column" label="Select column with base location" type="data_column" numerical="false" data_ref="input" /> | |
| 47 <param name="base_column" label="Select column with base to concatenate" type="data_column" numerical="false" data_ref="input" /> | |
| 48 <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" /> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 <param name="coverage" type="integer" value="3" label="Do not report bases with coverage less than:" /> | |
| 52 </inputs> | |
| 53 <outputs> | |
| 54 <data format="tabular" name="output" /> | |
| 55 </outputs> | |
| 56 <tests> | |
| 57 <test> | |
| 58 <param name="input" value="pileup_interval_in1.tabular" /> | |
| 59 <param name="format" value="six" /> | |
| 60 <param name="coverage" value="3" /> | |
| 61 <output name="output" file="pileup_interval_out1.tabular" /> | |
| 62 </test> | |
| 63 <test> | |
| 64 <param name="input" value="pileup_interval_in2.tabular" /> | |
| 65 <param name="format" value="ten" /> | |
| 66 <param name="which_base" value="first" /> | |
| 67 <param name="coverage" value="3" /> | |
| 68 <output name="output" file="pileup_interval_out2.tabular" /> | |
| 69 </test> | |
| 70 <test> | |
| 71 <param name="input" value="pileup_interval_in2.tabular" /> | |
| 72 <param name="format" value="manual" /> | |
| 73 <param name="seq_column" value="1" /> | |
| 74 <param name="loc_column" value="2" /> | |
| 75 <param name="base_column" value="3" /> | |
| 76 <param name="cvrg_column" value="8" /> | |
| 77 <param name="coverage" value="3" /> | |
| 78 <output name="output" file="pileup_interval_out2.tabular" /> | |
| 79 </test> | |
| 80 </tests> | |
| 81 <help> | |
| 82 | |
| 83 **What is does** | |
| 84 | |
| 85 Reduces 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). | |
| 86 | |
| 87 -------- | |
| 88 | |
| 89 **Types of pileup datasets** | |
| 90 | |
| 91 The 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. | |
| 92 | |
| 93 .. _SAMTools: http://samtools.sourceforge.net/pileup.shtml | |
| 94 | |
| 95 **Six column pileup**:: | |
| 96 | |
| 97 1 2 3 4 5 6 | |
| 98 --------------------------------- | |
| 99 chrM 412 A 2 ., II | |
| 100 chrM 413 G 4 ..t, IIIH | |
| 101 chrM 414 C 4 ...a III2 | |
| 102 chrM 415 C 4 TTTt III7 | |
| 103 | |
| 104 where:: | |
| 105 | |
| 106 Column Definition | |
| 107 ------ ---------------------------- | |
| 108 1 Chromosome | |
| 109 2 Position (1-based) | |
| 110 3 Reference base at that position | |
| 111 4 Coverage (# reads aligning over that position) | |
| 112 5 Bases within reads where (see Galaxy wiki for more info) | |
| 113 6 Quality values (phred33 scale, see Galaxy wiki for more) | |
| 114 | |
| 115 **Ten column pileup** | |
| 116 | |
| 117 The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: | |
| 118 | |
| 119 | |
| 120 1 2 3 4 5 6 7 8 9 10 | |
| 121 ------------------------------------------------ | |
| 122 chrM 412 A A 75 0 25 2 ., II | |
| 123 chrM 413 G G 72 0 25 4 ..t, IIIH | |
| 124 chrM 414 C C 75 0 25 4 ...a III2 | |
| 125 chrM 415 C T 75 75 25 4 TTTt III7 | |
| 126 | |
| 127 where:: | |
| 128 | |
| 129 Column Definition | |
| 130 ------- ---------------------------- | |
| 131 1 Chromosome | |
| 132 2 Position (1-based) | |
| 133 3 Reference base at that position | |
| 134 4 Consensus bases | |
| 135 5 Consensus quality | |
| 136 6 SNP quality | |
| 137 7 Maximum mapping quality | |
| 138 8 Coverage (# reads aligning over that position) | |
| 139 9 Bases within reads where (see Galaxy wiki for more info) | |
| 140 10 Quality values (phred33 scale, see Galaxy wiki for more) | |
| 141 | |
| 142 | |
| 143 .. __: http://samtools.sourceforge.net/cns0.shtml | |
| 144 | |
| 145 ------ | |
| 146 | |
| 147 **The output format** | |
| 148 | |
| 149 The 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. | |
| 150 | |
| 151 Given the following input with minimum coverage set to 3:: | |
| 152 | |
| 153 1 2 3 4 5 6 | |
| 154 --------------------------------- | |
| 155 chr1 112 G 3 ..Ta III6 | |
| 156 chr1 113 T 2 aT.. III5 | |
| 157 chr1 114 A 5 ,,.. IIH2 | |
| 158 chr1 115 C 4 ,., III | |
| 159 chrM 412 A 2 ., II | |
| 160 chrM 413 G 4 ..t, IIIH | |
| 161 chrM 414 C 4 ...a III2 | |
| 162 chrM 415 C 4 TTTt III7 | |
| 163 chrM 490 T 3 a I | |
| 164 | |
| 165 the following would be the output:: | |
| 166 | |
| 167 1 2 3 4 | |
| 168 ------------------- | |
| 169 chr1 111 112 G | |
| 170 chr1 113 115 AC | |
| 171 chrM 412 415 GCC | |
| 172 chrM 489 490 T | |
| 173 | |
| 174 where:: | |
| 175 | |
| 176 Column Definition | |
| 177 ------- ---------------------------- | |
| 178 1 Chromosome | |
| 179 2 Starting position (0-based) | |
| 180 3 Ending position (1-based) | |
| 181 4 Sequence of bases | |
| 182 | |
| 183 </help> | |
| 184 </tool> |