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1 <?xml version="1.0"?>
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2 <tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1">
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3 <description>BAM datasets and perform other transformations</description>
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4 <requirements>
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5 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
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6 <requirement type="package" version="0.1.18">samtools</requirement>
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7 </requirements>
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8
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9 <command>
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10 ##set up input files
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11
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12 #for $bam_count, $input_bam in enumerate( $input_bams ):
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13 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
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14 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
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15 #end for
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16
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17 #if str( $analysis_type.analysis_type_selector ) == "convert":
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18 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
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19 #set $reference_fasta_filename = "localref.fa"
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20 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
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21 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
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22 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
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23 #else:
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24 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
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25 #end if
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26 #end if
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27 #end if
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28
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29 ##finished setting up inputs
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30
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31 ##start bamtools commandline
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32
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33 bamtools
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34
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35 #if str( $analysis_type.analysis_type_selector ) == "convert":
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36
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37 convert
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38
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39 -format ${analysis_type.format_type.format_type_selector}
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40
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41 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
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42
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43 ${analysis_type.format_type.mapqual}
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44 -fasta "${reference_fasta_filename}"
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45
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46 #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
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47
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48 ${analysis_type.format_type.noheader}
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49
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50 #end if
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51
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52 -out $out_file1
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53
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54 #elif str( $analysis_type.analysis_type_selector ) == "count":
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55
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56 count
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57 > $out_file1
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58
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59 #elif str( $analysis_type.analysis_type_selector ) == "coverage":
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60
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61 coverage
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62 -out $out_file1
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63
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64 #elif str( $analysis_type.analysis_type_selector ) == "header":
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65
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66 header
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67 > $out_file1
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68
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69 #elif str( $analysis_type.analysis_type_selector ) == "merge":
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70
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71 merge
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72 -out $out_file1
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73
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74 #elif str( $analysis_type.analysis_type_selector ) == "random":
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75
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76 random
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77 -n ${analysis_type.count}
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78 -seed ${analysis_type.seed}
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79 -out $out_file1
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80
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81 #elif str( $analysis_type.analysis_type_selector ) == "revert":
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82
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83 revert
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84 ${analysis_type.keepDuplicate}
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85 ${analysis_type.keepQualities}
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86 -out $out_file1
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87
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88 #elif str( $analysis_type.analysis_type_selector ) == "sort":
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89
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90 sort
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91 ${analysis_type.byname}
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92 -out $out_file1
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93
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94 #end if
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95
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96 #for $bam_count, $input_bam in enumerate( $input_bams ):
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97 -in "localbam_${bam_count}.bam"
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98 #end for
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99
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100
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101 </command>
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102 <inputs>
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103
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104 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
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105 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
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106 </repeat>
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107
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108 <conditional name="analysis_type">
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109 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
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110 <option value="convert">Convert</option>
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111 <option value="count">Count</option>
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112 <option value="coverage">Coverage</option>
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113 <option value="header">Header</option>
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114 <option value="merge">Merge</option>
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115 <option value="random">Random</option>
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116 <option value="revert">Revert</option>
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117 <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
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118 <!-- Allowing users for sort files may break donstream functionality. -->
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119 <!-- To enable sort option simply uncomment the line below: -->
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120 <!-- <option value="sort">Sort</option> -->
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121 </param>
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122 <when value="convert">
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123 <conditional name="format_type">
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124 <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
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125 <option value="bed">BED</option>
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126 <option value="fasta">FASTA</option>
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127 <option value="fastq">FASTQ</option>
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128 <option value="json">JSON</option>
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129 <option value="pileup">Pileup</option>
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130 <option value="sam">SAM</option>
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131 <option value="yaml">YAML</option>
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132 </param>
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133 <when value="pileup">
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134 <conditional name="reference_source">
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135 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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136 <option value="cached">Locally cached</option>
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137 <option value="history">History</option>
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138 </param>
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139 <when value="cached">
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140 <param name="ref_file" type="select" label="Using reference genome">
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141 <options from_data_table="sam_fa_indexes">
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142 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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143 </options>
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144 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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145 </param>
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146 </when>
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147 <when value="history"> <!-- FIX ME!!!! -->
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148 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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149 </when>
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150 </conditional>
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151 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
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152 </when>
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153 <when value="sam">
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154 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
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155 </when>
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156 </conditional>
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157 </when>
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158 <when value="count">
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159 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
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160 </when>
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161 <when value="coverage">
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162 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
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163 </when>
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164 <when value="header">
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165 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
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166 </when>
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167 <when value="merge">
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168 <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
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169 </when>
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170 <when value="random">
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171 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
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172 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
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173 </when>
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174 <when value="revert">
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175 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
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176 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
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177 </when>
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178 <when value="sort">
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179 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
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180 </when>
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181 </conditional>
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182
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183 </inputs>
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184 <outputs>
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185 <data format="txt" name="out_file1">
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186 <change_format>
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187 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
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188 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
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189 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
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190 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
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191 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
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192 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
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193 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
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194 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
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195 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
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196 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
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197 </change_format>
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198 </data>
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199 </outputs>
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200 <tests>
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201 <test>
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202 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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203 <param name="analysis_type_selector" value="convert"/>
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204 <param name="format_type_selector" value="pileup"/>
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205 <param name="reference_source_selector" value="history" />
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206 <param name="mapqual" value="true" />
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207 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
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208 <output name="output_bam" file="bamtools-convert-pileup.pu" />
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209 </test>
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210 <test>
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211 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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212 <param name="analysis_type_selector" value="count"/>
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213 <output name="output_bam" file="bamtools-count.tab" />
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214 </test>
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215 <test>
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216 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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217 <param name="analysis_type_selector" value="coverage"/>
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218 <output name="output_bam" file="bamtools-coverage.tab" />
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219 </test>
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220 <test>
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221 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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222 <param name="analysis_type_selector" value="header"/>
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223 <output name="output_bam" file="bamtools-header.txt" />
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224 </test>
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225 </tests>
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226
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227 <stdio>
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228 <exit_code range="1:" />
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229 </stdio>
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230
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231 <help>
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232
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233 **What is does**
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234
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235 BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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236 This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.
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237
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238 -----
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239
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240 **Convert**
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241
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242 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
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243 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
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244
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245 -----
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246
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247 **Count**
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248
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249 Counts a number of alignments in a BAM dataset(s).
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250
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251 -----
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252
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253 **Coverage**
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254
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255 Prints per-base coverage for a BAM dataset.
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256
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257 -----
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258
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259 **Header**
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260
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261 Prints header from a BAM dataset(s).
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262
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263 ------
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264
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265 **Merge**
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266
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267 Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.
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268
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269 ------
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270
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271 **Random**
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272
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273 Grabs a specified number of random lines from BAM dataset(s).
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274
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275 ------
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276
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277 **Revert**
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278
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279 Removes duplicate marks and restores original (non-recalibrated) base qualities.
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280
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281 -----
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282
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283 .. class:: infomark
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284
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285 **More information**
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286
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287 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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288
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289 </help>
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290 <citations>
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291 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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292 </citations>
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293 </tool>
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