Mercurial > repos > blankenberg > naive_variant_caller

annotate naive_variant_caller.xml @ 15:aff38ea879f1 draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit dfca863a9a361877d6d98b92072f1ebc316c5767
author blankenberg
date Wed, 28 Feb 2018 16:01:52 -0500
parents 5c852eca82e0
children 07e71cf6c8ef
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1 <tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3">
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2 <description> - tabulate variable sites from BAM datasets</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.3">nvc</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 <exit_code range=":-1" />
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9 </stdio>
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10 <version_command>naive_variant_caller.py --version</version_command>
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11 <command>naive_variant_caller.py
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12 -o "${output_vcf}"
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14 #for $input_bam in $reference_source.input_bams:
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15 -b '${input_bam.input_bam}'
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16 -i '${input_bam.input_bam.metadata.bam_index}'
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17 #end for
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19 #if $reference_source.reference_source_selector != "history":
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20 -r '${reference_source.ref_file.fields.path}'
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21 #elif $reference_source.ref_file:
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22 -r '${reference_source.ref_file}'
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23 #end if
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25 #for $region in $regions:
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26 --region '${region.chromosome}:${region.start}-${region.end}'
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27 #end for
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29 #for $region_file in $region_files:
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30 --regions_filename '${region_file.input_region}'
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31 --regions_file_columns '${int($region_file.input_region.metadata.chromCol)-1},${int($region_file.input_region.metadata.startCol)-1},${int($region_file.input_region.metadata.endCol)-1}'
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32 #end for
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34 ${variants_only}
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36 ${use_strand}
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38 --ploidy '${$ploidy}'
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40 --min_support_depth '${min_support_depth}'
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41
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42 #if str($min_base_quality):
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43 --min_base_quality '${min_base_quality}'
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44 #end if
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45
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46 #if str($min_mapping_quality):
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47 --min_mapping_quality '${min_mapping_quality}'
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48 #end if
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49
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50 --allow_out_of_bounds_positions
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51
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52 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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53 #if str( $advanced_options.coverage_dtype ) != "guess":
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54 --coverage_dtype '${advanced_options.coverage_dtype}'
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55 #end if
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56 ${advanced_options.safe}
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57 #end if
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58 </command>
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59 <inputs>
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60 <conditional name="reference_source">
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61 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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62 <option value="cached">Locally cached</option>
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63 <option value="history">History</option>
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64 </param>
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65 <when value="cached">
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66 <repeat name="input_bams" title="BAM file" min="1" >
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67 <param name="input_bam" type="data" format="bam" label="BAM file">
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68 <validator type="unspecified_build" />
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69 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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70 </param>
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71 </repeat>
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72 <param name="ref_file" type="select" label="Using reference genome" >
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73 <options from_data_table="sam_fa_indexes">
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74 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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75 </options>
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76 <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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77 </param>
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78 </when>
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79 <when value="history"> <!-- FIX ME!!!! -->
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80 <repeat name="input_bams" title="BAM file" min="1" >
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81 <param name="input_bam" type="data" format="bam" label="BAM file" >
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82 </param>
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83 </repeat>
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84 <param name="ref_file" type="data" format="fasta" label="Using reference file" optional="True" />
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85 </when>
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86 </conditional>
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87
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88 <repeat name="regions" title="Restrict to regions" min="0" >
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89 <param name="chromosome" type="text" value="" optional="False" label="Chromosome" />
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90 <param name="start" type="integer" value="" optional="True" label="Start" help="0-based, closed. (BED style)" />
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91 <param name="end" type="integer" value="" optional="True" label="End" help="0-based, open. (BED style)" />
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92 </repeat>
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93
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94 <repeat name="region_files" title="Restrict to regions by file" min="0" >
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95 <param name="input_region" type="data" format="interval" label="Genomic Regions" />
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96 </repeat>
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97
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98 <!-- TODO: enhance filtering -->
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99 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
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100 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
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101 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
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102
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103 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
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104 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/>
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105
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106 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
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107
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108 <conditional name="advanced_options">
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109 <param name="advanced_options_selector" type="select" label="Show Advanced Options">
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110 <option value="basic" selected="True">Hide Advanced Options</option>
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111 <option value="advanced">Show Advanced Options</option>
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112 </param>
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113 <when value="basic">
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114 <!-- Do nothing here -->
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115 </when>
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116 <when value="advanced">
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117 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
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118 <option value="guess" selected="True">Guess</option>
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119 <option value="uint8">uint8</option>
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120 <option value="uint16">uint16</option>
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121 <option value="uint32">uint32</option>
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122 <option value="uint64">uint64</option>
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123 </param>
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124 <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
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125 </when>
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126 </conditional>
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127
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128 </inputs>
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129 <outputs>
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130 <data format="vcf" name="output_vcf" />
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131 </outputs>
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132 <tests>
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133 <test>
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134 <param name="reference_source_selector" value="history" />
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135 <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
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136 <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
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137 <param name="regions" value="0" />
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138 <param name="min_support_depth" value="0" />
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139 <param name="min_base_quality" value="" />
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140 <param name="min_mapping_quality" value="" />
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141 <param name="ploidy" value="2" />
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142 <param name="variants_only" value="False" />
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143 <param name="use_strand" value="False" />
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144 <param name="advanced_options_selector" value="advanced" />
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145 <param name="coverage_dtype" value="uint8" />
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146 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
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147 </test>
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148 </tests>
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149 <help>
15
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150 The **Naive Variant Caller** tool (NVC).
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151
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152 ------
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153
14
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154 **What it does**
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155
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156 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples.
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157
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158 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately.
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159
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160 In addition to calling alternate alleles based upon simple ratios of nucleotides at a position, per base nucleotide counts are also provided. A custom tag, NC, is used within the Genotype fields. The NC field is a comma-separated listing of nucleotide counts in the form of &lt;nucleotide&gt;=&lt;count&gt;, where a plus or minus character is prepended to indicate strand, if the strandedness option was specified.
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161
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162
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163 ------
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164
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165 **Inputs**
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166
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167 Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
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168
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169
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170 **Outputs**
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171
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172 The output is in VCF format.
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173
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174 Example VCF output line, without reporting by strand:
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175 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
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176
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177 Example VCF output line, when reporting by strand:
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178 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
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179
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180 **Options**
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181
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182 Reference Genome:
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183
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184 Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
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185
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186 Restrict to regions:
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187
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188 You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions.
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189
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190 Minimum number of reads needed to consider a REF/ALT:
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191
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192 This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
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193
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194 Minimum base quality:
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195
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196 The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
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197
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198 Minimum mapping quality:
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199
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200 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
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201
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202 Ploidy:
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203
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204 The number of genotype calls to make at each reported position.
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205
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206 Only write out positions with possible alternate alleles:
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207
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208 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
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209
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210 Report counts by strand:
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211
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212 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
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213
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214 Choose the dtype to use for storing coverage information:
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215
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216 This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
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217
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218 +--------+----------------------------+
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219 | name | maximum coverage value |
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220 +========+============================+
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221 | uint8 | 255 |
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222 +--------+----------------------------+
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223 | uint16 | 65,535 |
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224 +--------+----------------------------+
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225 | uint32 | 4,294,967,295 |
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226 +--------+----------------------------+
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227 | uint64 | 18,446,744,073,709,551,615 |
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228 +--------+----------------------------+
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229
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230
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231 </help>
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232 <citations>
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233 <citation type="doi">10.1186/gb4161</citation>
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234 </citations>
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235
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236 </tool>