/tools/samtools/sam_pileup.xml
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1<tool id="sam_pileup" name="Generate pileup" version="1.1.1"> 2 <description>from BAM dataset</description> 3 <requirements> 4 <requirement type="package">samtools</requirement> 5 </requirements> 6 <command interpreter="python"> 7 sam_pileup.py 8 --input1=$input1 9 --output=$output1 10 --ref=$refOrHistory.reference 11 #if $refOrHistory.reference == "history": 12 --ownFile=$refOrHistory.ownFile 13 #else: 14 --ownFile="None" 15 #end if 16 --dbkey=${input1.metadata.dbkey} 17 --indexDir=${GALAXY_DATA_INDEX_DIR} 18 --bamIndex=${input1.metadata.bam_index} 19 --lastCol=$lastCol 20 --indels=$indels 21 --mapCap=$mapCap 22 --consensus=$c.consensus 23 #if $c.consensus == "yes": 24 --theta=$c.theta 25 --hapNum=$c.hapNum 26 --fraction=$c.fraction 27 --phredProb=$c.phredProb 28 #else: 29 --theta="None" 30 --hapNum="None" 31 --fraction="None" 32 --phredProb="None" 33 #end if 34 </command> 35 <inputs> 36 <conditional name="refOrHistory"> 37 <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?"> 38 <option value="indexed">Use a built-in index</option> 39 <option value="history">Use one from the history</option> 40 </param> 41 <when value="indexed"> 42 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> 43 <validator type="unspecified_build" /> 44 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> 45 </param> 46 </when> 47 <when value="history"> 48 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> 49 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> 50 </when> 51 </conditional> 52 <param name="lastCol" type="select" label="Whether or not to print the mapping quality as the last column" help="Makes the output easier to parse, but is space inefficient"> 53 <option value="no">Do not print the mapping quality as the last column</option> 54 <option value="yes">Print the mapping quality as the last column</option> 55 </param> 56 <param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels"> 57 <option value="no">Print all lines</option> 58 <option value="yes">Print only lines containing indels</option> 59 </param> 60 <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> 61 <conditional name="c"> 62 <param name="consensus" type="select" label="Call consensus according to MAQ model?"> 63 <option selected="true" value="no">No</option> 64 <option value="yes">Yes</option> 65 </param> 66 <when value="no" /> 67 <when value="yes"> 68 <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" /> 69 <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> 70 <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> 71 <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> 72 </when> 73 </conditional> 74 </inputs> 75 <outputs> 76 <data format="tabular" name="output1" label="${tool.name} on ${on_string}: converted pileup" /> 77 </outputs> 78 <tests> 79 <test> 80 <!-- 81 Bam to pileup command: 82 samtools faidx chr_m.fasta 83 samtools pileup -M 60 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out1.pileup 84 chr_m.fasta is the prefix of the index 85 --> 86 <param name="reference" value="history" /> 87 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" /> 88 <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> 89 <param name="lastCol" value="no" /> 90 <param name="indels" value="no" /> 91 <param name="mapCap" value="60" /> 92 <param name="consensus" value="no" /> 93 <output name="output1" file="sam_pileup_out1.pileup" /> 94 </test> 95 <test> 96 <!-- 97 Bam to pileup command: 98 samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup 99 chr_m.fasta is the prefix of the index 100 --> 101 <param name="reference" value="indexed" /> 102 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> 103 <param name="lastCol" value="no" /> 104 <param name="indels" value="no" /> 105 <param name="mapCap" value="60" /> 106 <param name="consensus" value="yes" /> 107 <param name="theta" value="0.85" /> 108 <param name="hapNum" value="2" /> 109 <param name="fraction" value="0.001" /> 110 <param name="phredProb" value="40" /> 111 <output name="output1" file="sam_pileup_out2.pileup" /> 112 </test> 113 </tests> 114 <help> 115 116**What it does** 117 118Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below. 119 120.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml 121 122------ 123 124**Types of pileup datasets** 125 126The description of pileup format below is largely based on information that can be found on SAMTools Pileup_ documentation page. The 6- and 10-column variants are described below. 127 128.. _Pileup: http://samtools.sourceforge.net/pileup.shtml 129 130**Six column pileup**:: 131 132 1 2 3 4 5 6 133 --------------------------------- 134 chrM 412 A 2 ., II 135 chrM 413 G 4 ..t, IIIH 136 chrM 414 C 4 ...a III2 137 chrM 415 C 4 TTTt III7 138 139where:: 140 141 Column Definition 142 ------- ---------------------------- 143 1 Chromosome 144 2 Position (1-based) 145 3 Reference base at that position 146 4 Coverage (# reads aligning over that position) 147 5 Bases within reads where (see Galaxy wiki for more info) 148 6 Quality values (phred33 scale, see Galaxy wiki for more) 149 150**Ten column pileup** 151 152The `ten-column` (consensus_) pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: 153 154 155 1 2 3 4 5 6 7 8 9 10 156 ------------------------------------------------ 157 chrM 412 A A 75 0 25 2 ., II 158 chrM 413 G G 72 0 25 4 ..t, IIIH 159 chrM 414 C C 75 0 25 4 ...a III2 160 chrM 415 C T 75 75 25 4 TTTt III7 161 162where:: 163 164 Column Definition 165 ------- -------------------------------------------------------- 166 1 Chromosome 167 2 Position (1-based) 168 3 Reference base at that position 169 4 Consensus bases 170 5 Consensus quality 171 6 SNP quality 172 7 Maximum mapping quality 173 8 Coverage (# reads aligning over that position) 174 9 Bases within reads where (see Galaxy wiki for more info) 175 10 Quality values (phred33 scale, see Galaxy wiki for more) 176 177 178.. _consensus: http://samtools.sourceforge.net/cns0.shtml 179 180 181 </help> 182</tool> 183 184