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1 <tool id="sam_pileup" name="Generate pileup" version="1.1.1">
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2 <description>from BAM dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.16">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" label="${tool.name} on ${on_string}: converted pileup" />
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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 > 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 > 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
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182 **Citation**
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183
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184 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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185
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186
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187 </help>
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188 </tool>
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189
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190
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