Mercurial > repos > wolma > mimodd_core

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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 16:39:44 -0500
parents 85576338fbcf
children
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1 <tool id="mimodd_varextract" name="MiModD Extract Variant Sites"
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2 version="@MIMODD_WRAPPER_VERSION@">
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3 <description>from a BCF file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 mimodd varextract '$ifile'
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12 #if $len($sitesinfo)
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13 -p
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14 #for $source in $sitesinfo
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15 '${source.pre_vcf}'
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16 #end for
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17 #end if
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18 --ofile '$output_vcf'
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19 $keep_alts
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20 --verbose
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21 ]]></command>
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22
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23 <inputs>
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24 <param name="ifile" type="data" format="bcf" label="BCF input file"
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25 help="Use the MiModD Variant Calling tool to generate the input for this tool."/>
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26 <repeat name="sitesinfo" title="include information from pre-calculated vcf dataset" default="0">
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27 <param name="pre_vcf" type="data" format="vcf"
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28 label="independently generated vcf datset" />
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29 </repeat>
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30 <param name="keep_alts" type="boolean" truevalue="-a" falsevalue="" checked="false"
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31 label="keep all sites with alternate bases"
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32 help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." />
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33 </inputs>
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34 <outputs>
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35 <data name="output_vcf" format="vcf"
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36 label="Variants extracted with MiModd from ${on_string}"/>
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="ifile" value="a.bcf" />
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42 <output name="output_vcf" ftype="vcf">
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43 <assert_contents>
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44 <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.N2.ot266" />
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45 </assert_contents>
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46 </output>
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47 <assert_command>
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48 <not_has_text text="-a" />
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49 </assert_command>
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50 </test>
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51 <test>
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52 <param name="ifile" value="a_part2.bcf" />
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53 <param name="keep_alts" value="true" />
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54 <param name="pre_vcf" value="a.vcf" />
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55 <output name="output_vcf" ftype="vcf">
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56 <assert_contents>
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57 <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.ot266.external_source_1_N2.external_source_1_ot266" />
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58 </assert_contents>
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59 </output>
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60 <assert_command>
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61 <has_text text="-a" />
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62 </assert_command>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 .. class:: infomark
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67
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68 **What it does**
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69
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70 The tool takes as input a BCF dataset like the ones produced by the
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71 *MiModD Variant Calling* tool, extracts just the variant sites from it and
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72 reports them in VCF format.
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73
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74 If the BCF input file specifies multiple samples, sites are included if they qualify as variant sites in at least one sample.
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75
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76 ----------
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77
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78 **Options:**
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79
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80 **keep all sites with alternate bases**
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81
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82 By default, a variant site is considered to be a position in the genome for
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83 which a non-reference allele appears in the inferred genotype of any sample.
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84
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85 You can select the *keep all sites with alternate bases* option, if instead
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86 you want to extract all sites, for which at least one non-reference base has
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87 been observed (whether resulting in a non-reference allele call or not).
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88 Using this option should rarely be necessary, but could be occassionally
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89 helpful for closer inspection of candidate genomic regions.
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90
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91
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92 **include information from pre-calculated vcf dataset**
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93
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94 During the process of variant extraction the tool can take into account
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95 genome positions specified in one or more independently generated VCF datasets.
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96 If such additional VCF input is provided, the tool output will contain the
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97 samples found in these files as additional samples and sites from the main BCF
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98 dataset will be included not only if they qualify as variant sites in at least
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99 one sample specified in the BCF, but also if they are listed in any of the
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100 additional VCF datasets.
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101
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102 Optional VCF input can be particularly useful in one of the following
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103 situations:
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104
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105 1) you have prior information that leads you to think that certain genome
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106 positions are of special relevance for your project and, thus, you are
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107 interested in the statistics produced by the variant caller for these
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108 positions even if they are not considered variant sites. In this case you
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109 can use a minimal VCF dataset to guide the variant extraction process to
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110 include these positions. This dataset needs a minimal header of the form:
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111
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112 ``##fileformat=VCFv4.2``
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113
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114 followed by positional information like in this example::
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115
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116 #CHROM POS ID REF ALT QUAL FILTER INFO
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117 chrI 1222 . . . . . .
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118 chrI 2651 . . . . . .
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119 chrI 3659 . . . . . .
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120 chrI 3731 . . . . . .
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121
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122 , where columns are tab-separated and . serves as a placeholder for missing
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123 information.
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124
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125 2) you have actual variant calls from an additional sample, but you do not
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126 have access to the original sequenced reads data (if you had, the
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127 recommended approach would be to include that data in the
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128 *MiModD Variant Calling* step.
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129
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130 This situation is often encountered with published datasets. Assume you
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131 have obtained a list of known single nucleotide variants (SNVs) found in
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132 one particular strain of your favorite model organism and you would like
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133 to know which of these SNVs are present in the related strains you have
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134 sequenced. You have aligned the sequenced reads from your samples and have
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135 used the *MiModD Variant Calling* tool, which has generated a BCF dataset
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136 ready for variant extraction. If the SNV list for the previously sequenced
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137 strain is in VCF format already, you can now just plug it into the
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138 analysis process by specifying it in the tool interface as an
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139 *independently generated vcf dataset*.
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140 The resulting vcf output will contain all SNV sites along with the variant
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141 sites found in the BCF alone. You can then proceed to the
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142 *MiModD VCF Filter* tool to look at the original SNV sites only or to
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143 investigate any other interesting subset of sites. If the SNV list is in
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144 some other format, you will have o convert it to VCF first. At a minimum,
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145 the dataset must have a ``##fileformat`` header line like the previous
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146 example and have the ``REF`` and ``ALT`` column filled in like so::
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147
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148 #CHROM POS ID REF ALT QUAL FILTER INFO
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149 chrI 1897409 . A G . . .
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150 chrI 1897492 . C T . . .
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151 chrI 1897616 . C A . . .
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152 chrI 1897987 . A T . . .
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153 chrI 1898185 . C T . . .
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154 chrI 1898715 . G A . . .
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155 chrI 1898729 . T C . . .
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156 chrI 1900288 . T A . . .
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157
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158 , in which case the tool will assume that the corresponding sample is
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159 homozygous for each of the SNVs.
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160 If you need to distinguish between homozygous and heterozygous SNVs you
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161 will have to extend the format to include a format and a sample column
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162 with genotype (GT) information like in this example::
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163
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164 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sampleX
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165 chrI 1897409 . A G . . . GT 1/1
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166 chrI 1897492 . C T . . . GT 0/1
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167 chrI 1897616 . C A . . . GT 0/1
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168 chrI 1897987 . A T . . . GT 0/1
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169 chrI 1898185 . C T . . . GT 0/1
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170 chrI 1898715 . G A . . . GT 0/1
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171 chrI 1898729 . T C . . . GT 0/1
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172 chrI 1900288 . T A . . . GT 0/1
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173
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174 , in which sampleX would be heterozygous for all SNVs except the first.
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175
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176 .. class:: warningmark
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177
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178 If the optional VCF input contains INDEL calls, these will be ignored by the
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179 tool.
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180
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181 @HELP_FOOTER@
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182 ]]></help>
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183 <expand macro="citations" />
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184 </tool>