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Bug fixes for Draw variants, Phylip, and gd_d_tools
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 13:46:10 -0500
parents a631c2f6d913
children 51cd0307fb70
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1 <tool id="gd_make_phylip" name="Phylip" version="1.1.0" force_history_refresh="True">
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2 <description>: prepare data for phylogenetic analysis</description>
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3
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4 <command interpreter="python">
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5 #set $zero_based = 1
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6 #set $gen_chrClmn = int($input.metadata.ref) - $zero_based
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7 #set $gen_posClmn = int($input.metadata.rPos) - $zero_based
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8 #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1
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9 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2
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10 make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn'
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11 #if $input_type.choice == '0'
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12 #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based
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13 #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based
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14 #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1
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15 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2
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16 '--altrClmnCvrg=$cov_altrClmn' '--chrClmnCvrg=$cov_chrClmn' '--cvrgTreshold=$input_type.coverage_threshold' '--gd_indivs_cover=$indivs_input' '--indvlsPrctTrshld=$input_type.indivs_threshold' '--inputCover=$input_type.coverage_input' '--inputCover_type=$input_type.coverage_input.ext' '--posClmnCvrg=$cov_posClmn' '--refClmnCvrg=$cov_refClmn'
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17 #else if $input_type.choice == '1'
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18 #set $fchrClmn = int($input_type.annotation_input.metadata.chromCol) - $zero_based
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19 #set $strandClmn = int($input_type.annotation_input.metadata.strandCol) - $zero_based
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20 #set $geneNameClmn = int($input_type.annotation_input.metadata.nameCol) - $zero_based
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21 #set $txStartClmn = int(str($input_type.tx_start_col)) - $zero_based
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22 #set $txEndClmn = int(str($input_type.tx_end_col)) - $zero_based
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23 #set $cdsStartClmn = int(str($input_type.cds_start_col)) - $zero_based
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24 #set $cdsEndClmn = int(str($input_type.cds_end_col)) - $zero_based
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25 #set $startExsClmn = int(str($input_type.exs_start_col)) - $zero_based
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26 #set $endExsClmn = int(str($input_type.exs_end_col)) - $zero_based
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27 '--cdsEndClmn=$cdsEndClmn' '--cdsStartClmn=$cdsStartClmn' '--endExsClmn=$endExsClmn' '--fchrClmn=$fchrClmn' '--geneNameClmn=$geneNameClmn' '--gene_info=$input_type.annotation_input' '--sequence=$input_type.fasta_input' '--startExsClmn=$startExsClmn' '--strandClmn=$strandClmn' '--txEndClmn=$txEndClmn' '--txStartClmn=$txStartClmn'
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28 #end if
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29 </command>
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30
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31 <code file="make_phylip_hooks.py" />
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32
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33 <inputs>
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34 <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset">
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35 <validator type="metadata" check="scaffold" message="scaffold missing" />
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36 <validator type="metadata" check="pos" message="pos missing" />
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37 </param>
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38 <param name="indivs_input" type="data" format="gd_indivs" label="Individuals dataset" />
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39 <conditional name="input_type">
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40 <param name="choice" type="select" format="integer" label="Input type">
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41 <option value="0" selected="true">Coverage</option>
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42 <option value="1">Genes</option>
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43 </param>
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44 <when value="0">
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45 <param name="coverage_input" type="data" format="gd_genotype,gd_snp" label="Coverage dataset">
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46 <validator type="metadata" check="scaffold" message="scaffold missing" />
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47 <validator type="metadata" check="pos" message="pos missing" />
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48 </param>
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49 <param name="coverage_threshold" type="integer" min="1" value="1" label="Coverage threshold" />
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50 <param name="indivs_threshold" type="float" value="0.5" min="0.0" max="1.0" label="Individuals genotype percentage threshold" />
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51 </when>
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52 <when value="1">
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53 <param name="annotation_input" type="data" format="interval" label="Genes dataset">
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54 <validator type="metadata" check="chromCol" message="chromCol missing" />
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55 <validator type="metadata" check="strandCol" message="strandCol missing" />
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56 <validator type="metadata" check="nameCol" message="nameCol missing" />
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57 </param>
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58 <param name="tx_start_col" type="data_column" data_ref="input" label="Genes transcript start column" />
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59 <param name="tx_end_col" type="data_column" data_ref="input" label="Genes transcript end column" />
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60 <param name="cds_start_col" type="data_column" data_ref="input" label="Genes coding sequence start column" />
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61 <param name="cds_end_col" type="data_column" data_ref="input" label="Genes coding sequence end column" />
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62 <param name="exs_start_col" type="data_column" data_ref="input" label="Genes exon starts column" />
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63 <param name="exs_end_col" type="data_column" data_ref="input" label="Genes exon ends column" />
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64 <param name="fasta_input" type="data" format="fasta" label="FASTA dataset" />
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65 </when>
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66 </conditional>
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67 </inputs>
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68
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69 <outputs>
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70 <data name="output1" format="txt" />
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71 </outputs>
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72
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73 <help>
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74 **What it does**
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75
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76 This tool creates phylip formatted files from two different input types:
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77 coverage and genes.
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78
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79 If the coverage option is selected the inputs for the program are:
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80
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81 1. a gd_indivs table
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82 2. a gd_genotype file with the coverage information for individuals in the gd_indivs table
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83 3. a gd_genotype file with the genotype information for individuals in the gd_indivs table
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84 4. a coverage threshold (optional)
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85 5. a percentage of individuals (threshold).
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86
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87 The program produces a phylip formatted file using the sequence in the
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88 genotype file as a template. In this sequence nucleotides for each
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89 sequence that are below the coverage threshold, or the positions with
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90 a percentage of individuals below the selected value are replaced by "N".
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91
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92 If the gene option is selected the inputs for the program are:
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93
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94 1. a gd_indivs table
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95 2. a gene dataset table with a gene name in the first column
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96 3. the column with transcript start in the gene dataset table
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97 4. the column with transcript end in the gene dataset table
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98 5. the column with coding start in the gene dataset table
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99 6. the column with coding end in the gene dataset table
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100 7. the column with exon starts (comma-separated) in the gene dataset table
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101 8. the column with exon ends (comma-separated) in the gene dataset table
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102 9. a FASTA formatted file for all the genes of interest with their names as headers (NOTE: these names should be the same in the input gene dataset table).
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103
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104 The program produces as output one phylip formatted file for each gene
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105 in the gene dataset table.
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106
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107 -----
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108
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109 **Example**
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110
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111 In a case were the option coverage is selected, for the inputs:
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112
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113 - gd_indivs::
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114
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115 7 W_Java
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116 10 E_Java
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117 16 Pen_Ma
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118 ...
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119
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120 - Genotype table::
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121
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122 chrM 15 T C -1 -1 2 -1 -1 2 -1 -1 -1 -1 -1 2 -1 -1 -1 -1 0 -1 -1
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123 chrM 18 G A -1 -1 0 -1 -1 0 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1
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124 chrM 20 C T -1 -1 0 -1 -1 2 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1
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125 ...
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126
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127 - Coverage table::
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128
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129 chrM 0 G G 0 0 0 0 0 0 0 0 0 0 0 0 0
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130 chrM 1 T T 0 0 3 0 0 50 0 0 0 0 0 2 0
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131 chrM 2 T T 0 0 5 0 0 50 0 0 0 0 0 2 0
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132 ...
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133
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134 - Coverage threshold = 0
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135
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136 - Percentage of individuals = 0.0
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137
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138 - The output is::
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139
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140 4 19 15428
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141 W_Java GTTCATCATGTTCATCGAAT
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142 E_Java GTTCATCATGTTCATCGAAC
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143 Pen_Ma GTTCATCATGTTCATCGAAT
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144
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145 In a case were option genotype is selected with the inputs:
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146
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147 - Gene dataset table input::
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148
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149 1 ENSLAFT00000017123 chrM + 1002 1061 1002 1061 1 1002, 1061, 0 ENSLAFG00000017122 cmpl incmpl 0, BTRC ENSLAFT00000017123 ENSLAFP00000014355
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150 1 ENSLAFT00000037164 chrM - 1058 1092 1062 1073 1 1062,1068 1065,1073 0 ENSLAFG00000007680 cmpl cmpl 0, MYOF ENSLAFT00000037164 ENSLAFP00000025175 26509
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151 1 ENSLAFT00000008925 chrM + 990 1000 990 1000 1 990, 1000, 0 ENSLAFG00000008924 incmpl incmpl 0, PRKG1 ENSLAFT00000008925 ENSLAFP00000007492
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152 ...
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153
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154 In this table:
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155
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156 column with transcript start = 5
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157 column with transcript end = 6
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158 column with coding start = 7
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159 column with coding end = 8
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160 column with exon starts = 10
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161 column with exon ends = 11
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162
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163 - gd_indivs::
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164
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165 7 W_Java
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166 10 E_Java
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167 16 Pen_Ma
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168 ...
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169
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170 - Genotype table::
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171
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172 chrM 1005 T C -1 -1 2 -1 -1 2 -1 -1 -1 -1 -1 2 -1 -1 -1 -1 0 -1 -1
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173 chrM 1060 G A -1 -1 0 -1 -1 0 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1
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174 chrM 991 C T -1 -1 0 -1 -1 2 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1
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175 ...
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176
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177 The outputs are going to one file for each sequence in the input gene
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178 dataset table (as long as they are included in the input FASTA file).
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179 </help>
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180 </tool>