[2] | 1 | <tool id="sam_pileup" name="Generate pileup" version="1.1.0"> |
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| 2 | <description>from BAM dataset</description> |
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| 3 | <requirements> |
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| 4 | <requirement type="package">samtools</requirement> |
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| 5 | </requirements> |
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| 6 | <command interpreter="python"> |
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| 7 | sam_pileup.py |
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| 8 | --input1=$input1 |
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| 9 | --output=$output1 |
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| 10 | --ref=$refOrHistory.reference |
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| 11 | #if $refOrHistory.reference == "history": |
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| 12 | --ownFile=$refOrHistory.ownFile |
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| 13 | #else: |
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| 14 | --ownFile="None" |
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| 15 | #end if |
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| 16 | --dbkey=${input1.metadata.dbkey} |
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| 17 | --indexDir=${GALAXY_DATA_INDEX_DIR} |
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| 18 | --bamIndex=${input1.metadata.bam_index} |
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| 19 | --lastCol=$lastCol |
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| 20 | --indels=$indels |
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| 21 | --mapCap=$mapCap |
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| 22 | --consensus=$c.consensus |
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| 23 | #if $c.consensus == "yes": |
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| 24 | --theta=$c.theta |
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| 25 | --hapNum=$c.hapNum |
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| 26 | --fraction=$c.fraction |
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| 27 | --phredProb=$c.phredProb |
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| 28 | #else: |
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| 29 | --theta="None" |
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| 30 | --hapNum="None" |
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| 31 | --fraction="None" |
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| 32 | --phredProb="None" |
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| 33 | #end if |
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| 34 | </command> |
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| 35 | <inputs> |
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| 36 | <conditional name="refOrHistory"> |
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| 37 | <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?"> |
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| 38 | <option value="indexed">Use a built-in index</option> |
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| 39 | <option value="history">Use one from the history</option> |
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| 40 | </param> |
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| 41 | <when value="indexed"> |
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| 42 | <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> |
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| 43 | <validator type="unspecified_build" /> |
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| 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" /> |
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| 45 | </param> |
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| 46 | </when> |
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| 47 | <when value="history"> |
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| 48 | <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> |
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| 49 | <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> |
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| 50 | </when> |
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| 51 | </conditional> |
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| 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"> |
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| 53 | <option value="no">Do not print the mapping quality as the last column</option> |
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| 54 | <option value="yes">Print the mapping quality as the last column</option> |
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| 55 | </param> |
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| 56 | <param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels"> |
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| 57 | <option value="no">Print all lines</option> |
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| 58 | <option value="yes">Print only lines containing indels</option> |
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| 59 | </param> |
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| 60 | <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> |
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| 61 | <conditional name="c"> |
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| 62 | <param name="consensus" type="select" label="Call consensus according to MAQ model?"> |
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| 63 | <option selected="true" value="no">No</option> |
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| 64 | <option value="yes">Yes</option> |
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| 65 | </param> |
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| 66 | <when value="no" /> |
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| 67 | <when value="yes"> |
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| 68 | <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" /> |
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| 69 | <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> |
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| 70 | <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> |
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| 71 | <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> |
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| 72 | </when> |
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| 73 | </conditional> |
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| 74 | </inputs> |
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| 75 | <outputs> |
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| 76 | <data format="tabular" name="output1" /> |
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| 77 | </outputs> |
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| 78 | <tests> |
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| 79 | <test> |
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| 80 | <!-- |
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| 81 | Bam to pileup command: |
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| 82 | samtools faidx chr_m.fasta |
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| 83 | samtools pileup -M 60 -f chr_m.fasta test-data/sam_pileup_in1.bam > test-data/sam_pileup_out1.pileup |
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| 84 | chr_m.fasta is the prefix of the index |
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| 85 | --> |
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| 86 | <param name="reference" value="history" /> |
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| 87 | <param name="input1" value="sam_pileup_in1.bam" ftype="bam" /> |
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| 88 | <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> |
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| 89 | <param name="lastCol" value="no" /> |
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| 90 | <param name="indels" value="no" /> |
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| 91 | <param name="mapCap" value="60" /> |
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| 92 | <param name="consensus" value="no" /> |
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| 93 | <output name="output1" file="sam_pileup_out1.pileup" /> |
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| 94 | </test> |
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| 95 | <test> |
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| 96 | <!-- |
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| 97 | Bam to pileup command: |
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| 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 > test-data/sam_pileup_out2.pileup |
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| 99 | chr_m.fasta is the prefix of the index |
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| 100 | --> |
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| 101 | <param name="reference" value="indexed" /> |
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| 102 | <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> |
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| 103 | <param name="lastCol" value="no" /> |
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| 104 | <param name="indels" value="no" /> |
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| 105 | <param name="mapCap" value="60" /> |
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| 106 | <param name="consensus" value="yes" /> |
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| 107 | <param name="theta" value="0.85" /> |
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| 108 | <param name="hapNum" value="2" /> |
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| 109 | <param name="fraction" value="0.001" /> |
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| 110 | <param name="phredProb" value="40" /> |
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| 111 | <output name="output1" file="sam_pileup_out2.pileup" /> |
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| 112 | </test> |
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| 113 | </tests> |
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| 114 | <help> |
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| 115 | |
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| 116 | **What it does** |
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| 117 | |
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| 118 | Uses 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. |
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| 119 | |
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| 120 | .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml |
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| 121 | |
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| 122 | ------ |
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| 123 | |
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| 124 | **Types of pileup datasets** |
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| 125 | |
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| 126 | The 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. |
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| 127 | |
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| 128 | .. _Pileup: http://samtools.sourceforge.net/pileup.shtml |
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| 129 | |
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| 130 | **Six column pileup**:: |
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| 131 | |
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| 132 | 1 2 3 4 5 6 |
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| 133 | --------------------------------- |
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| 134 | chrM 412 A 2 ., II |
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| 135 | chrM 413 G 4 ..t, IIIH |
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| 136 | chrM 414 C 4 ...a III2 |
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| 137 | chrM 415 C 4 TTTt III7 |
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| 138 | |
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| 139 | where:: |
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| 140 | |
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| 141 | Column Definition |
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| 142 | ------- ---------------------------- |
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| 143 | 1 Chromosome |
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| 144 | 2 Position (1-based) |
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| 145 | 3 Reference base at that position |
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| 146 | 4 Coverage (# reads aligning over that position) |
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| 147 | 5 Bases within reads where (see Galaxy wiki for more info) |
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| 148 | 6 Quality values (phred33 scale, see Galaxy wiki for more) |
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| 149 | |
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| 150 | **Ten column pileup** |
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| 151 | |
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| 152 | The `ten-column` (consensus_) pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: |
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| 153 | |
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| 154 | |
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| 155 | 1 2 3 4 5 6 7 8 9 10 |
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| 156 | ------------------------------------------------ |
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| 157 | chrM 412 A A 75 0 25 2 ., II |
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| 158 | chrM 413 G G 72 0 25 4 ..t, IIIH |
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| 159 | chrM 414 C C 75 0 25 4 ...a III2 |
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| 160 | chrM 415 C T 75 75 25 4 TTTt III7 |
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| 161 | |
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| 162 | where:: |
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| 163 | |
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| 164 | Column Definition |
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| 165 | ------- -------------------------------------------------------- |
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| 166 | 1 Chromosome |
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| 167 | 2 Position (1-based) |
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| 168 | 3 Reference base at that position |
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| 169 | 4 Consensus bases |
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| 170 | 5 Consensus quality |
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| 171 | 6 SNP quality |
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| 172 | 7 Maximum mapping quality |
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| 173 | 8 Coverage (# reads aligning over that position) |
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| 174 | 9 Bases within reads where (see Galaxy wiki for more info) |
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| 175 | 10 Quality values (phred33 scale, see Galaxy wiki for more) |
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| 176 | |
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| 177 | |
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| 178 | .. _consensus: http://samtools.sourceforge.net/cns0.shtml |
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| 179 | |
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| 180 | |
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| 181 | </help> |
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| 182 | </tool> |
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| 183 | |
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| 184 | |
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