Mercurial > repos > jjohnson > ensembl_variant_report

annotate ensembl_variant_report.xml @ 2:f87fe6bc48f4 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 6b6e5c13531bf909c4c70b7f8f9e28b4206d9068-dirty
author jjohnson
date Mon, 18 Mar 2019 21:43:34 -0400
parents 9f4ea174ce3d
children 652d35c42bca
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1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.2.0">
0
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2 <requirements>
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3 <requirement type="package" version="1.40">gtf_to_genes</requirement>
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4 <requirement type="package" version="3.1.4">twobitreader</requirement>
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5 <requirement type="package" version="1.62">biopython</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 python '$__tool_directory__/ensembl_variant_report.py'
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12 #if $ref.ref_source == 'cached':
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13 --twobit="$ref.ref_loc.fields.path"
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14 #else
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15 --twobit="$ref.ref_file"
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16 #end if
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17 --gene_model="$gtf_file"
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18 #if $variant.fmt == 'vcf':
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19 --input="$variant.input_vcf"
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20 --format=snpeff
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21 #else
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22 --input="$variant.input_tsv"
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23 --pos_column=$variant.pos_column
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24 --ref_column=$variant.ref_column
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25 --alt_column=$variant.alt_column
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26 --transcript_column=$variant.transcript_column
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27 --dp_column=$variant.dp_column
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28 --dpr_column=$variant.dpr_column
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29 #end if
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30 #if str($filter.min_depth) != '':
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31 --min_depth=$filter.min_depth
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32 #end if
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33 #if str($filter.min_freq) != '':
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34 --min_freq=$filter.min_freq
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35 #end if
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36 #if str($report.readthrough) != '':
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37 --readthrough=$report.readthrough
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38 #end if
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39 #if str($report.leading_aa) != '':
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40 --leading_aa=$report.leading_aa
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41 #end if
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42 #if str($report.trailing_aa) != '':
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43 --trailing_aa=$report.trailing_aa
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44 #end if
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45 --output="$output"
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46 ]]></command>
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47 <inputs>
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48 <conditional name="variant">
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49 <param name="fmt" type="select" label="Input format for variants">
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50 <option value="vcf">snpEff vcf</option>
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51 <option value="tsv">tabular from snpsift extract</option>
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52 </param>
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53 <when value="vcf">
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54 <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
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55 </when>
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56 <when value="tsv">
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57 <param name="input_tsv" type="data" format="tabular" label="tabular file"/>
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58 <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/>
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59 <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/>
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60 <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/>
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61 <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/>
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62 <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/>
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63 <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
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64 </when>
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65 </conditional>
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66 <conditional name="ref">
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67 <param name="ref_source" type="select" label="Source for Genomic Data">
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68 <option value="cached">Locally cached</option>
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69 <option value="history">History</option>
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70 </param>
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71 <when value="cached">
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72 <param name="ref_loc" type="select" label="Select reference 2bit file">
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73 <options from_data_table="twobit" />
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74 </param>
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75 </when>
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76 <when value="history">
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77 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
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78 </when>
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79 </conditional>
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80 <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/>
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81 <section name="filter" expanded="false" title="Filter Options">
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82 <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report"
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83 help="If a value is entered, ignore variants with DP INFO field less than this value"/>
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84 <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"
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85 help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/>
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86 </section>
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87 <section name="report" expanded="false" title="Report Options">
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88 <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/>
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89 <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display"
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90 help="Ignored for frame shifts"/>
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91 <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display"
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92 help="Ignored for frame shifts"/>
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93 </section>
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94
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95 </inputs>
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96 <outputs>
2
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97 <data name="output" format="tabular" >
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98 <actions>
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99 <action name="column_names" type="metadata"
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100 default="Gene,Ref_location,Ref_seq,Var_seq,Frequency,DP,Ensemble_Gene_transcript,AA_pos,AA_var,Protein_len,Stop_Codon,Variant_Peptide,Transcipt_type"/>
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101 </actions>
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102 </data>
0
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="fmt" value="vcf"/>
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107 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
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108 <param name="ref_source" value="history"/>
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109 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
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110 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
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111 <output name="output">
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112 <assert_contents>
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113 <has_text text="MGGQ_A_SASNSFSRLH" />
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114 <not_has_text text="*REDHAAGPEA" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 <test>
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119 <param name="fmt" value="vcf"/>
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120 <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
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121 <param name="ref_source" value="history"/>
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122 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
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123 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
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124 <output name="output">
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125 <assert_contents>
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126 <has_text text="MGGQ_A_SASNSFSRLH" />
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127 <not_has_text text="*REDHAAGPEA" />
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128 </assert_contents>
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129 </output>
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130 </test>
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131 <test>
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132 <param name="fmt" value="vcf"/>
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133 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
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134 <param name="ref_source" value="history"/>
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135 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
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136 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
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137 <param name="readthrough" value="1"/>
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138 <output name="output">
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139 <assert_contents>
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140 <has_text text="MGGQ_A_SASNSFSRLH" />
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141 <has_text text="*REDHAAGPEA" />
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142 </assert_contents>
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143 </output>
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144 </test>
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145 <test>
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146 <param name="fmt" value="vcf"/>
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147 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
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148 <param name="ref_source" value="history"/>
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149 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
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150 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
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151 <param name="min_depth" value="100"/>
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152 <param name="min_freq" value=".80"/>
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153 <output name="output">
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154 <assert_contents>
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155 <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" />
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156 <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" />
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157 </assert_contents>
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158 </output>
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159 </test>
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160 <test>
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161 <param name="fmt" value="tsv"/>
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162 <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
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163 <param name="ref_source" value="history"/>
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164 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
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165 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
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166 <param name="pos_column" value="2"/>
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167 <param name="ref_column" value="3"/>
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168 <param name="alt_column" value="4"/>
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169 <param name="transcript_column" value="7"/>
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170 <param name="dp_column" value="8"/>
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171 <param name="dpr_column" value="9"/>
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172 <output name="output">
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173 <assert_contents>
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174 <has_text text="MGGQ_A_SASNSFSRLH" />
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175 <not_has_text text="*REDHAAGPEA" />
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176 </assert_contents>
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177 </output>
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178 </test>
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179 </tests>
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180 <help><![CDATA[
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181 Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
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182 Allows readthrough of stop codons, and reports the stop codons.
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183
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184 Input can be a snpEff vcf file using either ANN or EFF annotations.
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185 Alternatively, the input can be a tabular file that has columns:
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186
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187 - pos
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188 - ref
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189 - alt
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190 - Ensembl Transcript ID
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191 - Read Depth (DP)
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192 - AlleleDepth (DPR)
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193
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194 ]]></help>
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195 <citations>
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196 <citation type="doi">10.1093/bioinformatics/btt385</citation>
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197 </citations>
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198 </tool>