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annotate make_phylip.xml @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents a631c2f6d913
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1 <tool id="gd_make_phylip" name="Phylip" version="1.0.0" 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.scaffold) - $zero_based
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7 #set $gen_posClmn = int($input.metadata.pos) - $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=$input' '--output=$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.scaffold) - $zero_based
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13 #set $cov_posClmn = int($input_type.coverage_input.metadata.pos) - $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=$input_type.coverage_input' '--posClmnCvrg=$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 <inputs>
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32 <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset">
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33 <validator type="metadata" check="scaffold" message="scaffold missing" />
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34 <validator type="metadata" check="pos" message="pos missing" />
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35 </param>
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36 <param name="indivs_input" type="data" format="gd_indivs" label="Individuals dataset" />
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37 <conditional name="input_type">
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38 <param name="choice" type="select" format="integer" label="Input type">
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39 <option value="0" selected="true">Coverage</option>
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40 <option value="1">Genes</option>
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41 </param>
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42 <when value="0">
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43 <param name="coverage_input" type="data" format="gd_genotype,gd_snp" label="Coverage dataset">
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44 <validator type="metadata" check="scaffold" message="scaffold missing" />
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45 <validator type="metadata" check="pos" message="pos missing" />
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46 </param>
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47 <param name="coverage_threshold" type="integer" min="1" value="1" label="Coverage threshold" />
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48 <param name="indivs_threshold" type="float" value="0.5" min="0.0" max="1.0" label="Individuals genotype percentage threshold" />
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49 </when>
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50 <when value="1">
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51 <param name="annotation_input" type="data" format="interval" label="Genes dataset">
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52 <validator type="metadata" check="chromCol" message="chromCol missing" />
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53 <validator type="metadata" check="strandCol" message="strandCol missing" />
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54 <validator type="metadata" check="nameCol" message="nameCol missing" />
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55 </param>
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56 <param name="tx_start_col" type="data_column" data_ref="input" label="Genes transcript start column" />
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57 <param name="tx_end_col" type="data_column" data_ref="input" label="Genes transcript end column" />
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58 <param name="cds_start_col" type="data_column" data_ref="input" label="Genes coding sequence start column" />
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59 <param name="cds_end_col" type="data_column" data_ref="input" label="Genes coding sequence end column" />
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60 <param name="exs_start_col" type="data_column" data_ref="input" label="Genes exon starts column" />
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61 <param name="exs_end_col" type="data_column" data_ref="input" label="Genes exon ends column" />
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62 <param name="fasta_input" type="data" format="fasta" label="FASTA dataset" />
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63 </when>
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64 </conditional>
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65 </inputs>
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66
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67 <outputs>
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68 <data name="output1" format="txt" />
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69 </outputs>
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70
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71 <help>
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72 **What it does**
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73
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74 This tool creates phylip formatted files from two different input types:
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75 coverage and genes.
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76
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77 If the coverage option is selected the inputs for the program are:
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78
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79 1. a gd_indivs table
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80 2. a gd_genotype file with the coverage information for individuals in the gd_indivs table
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81 3. a gd_genotype file with the genotype information for individuals in the gd_indivs table
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82 4. a coverage threshold (optional)
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83 5. a percentage of individuals (threshold).
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84
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85 The program produces a phylip formatted file using the sequence in the
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86 genotype file as a template. In this sequence nucleotides for each
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87 sequence that are below the coverage threshold, or the positions with
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88 a percentage of individuals below the selected value are replaced by "N".
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89
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90 If the gene option is selected the inputs for the program are:
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91
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92 1. a gd_indivs table
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93 2. a gene dataset table with a gene name in the first column
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94 3. the column with transcript start in the gene dataset table
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95 4. the column with transcript end in the gene dataset table
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96 5. the column with coding start in the gene dataset table
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97 6. the column with coding end in the gene dataset table
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98 7. the column with exon starts (comma-separated) in the gene dataset table
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99 8. the column with exon ends (comma-separated) in the gene dataset table
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100 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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101
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102 The program produces as output one phylip formatted file for each gene
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103 in the gene dataset table.
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104
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105 -----
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106
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107 **Example**
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108
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109 In a case were the option coverage is selected, for the inputs:
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110
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111 - gd_indivs::
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112
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113 7 W_Java
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114 10 E_Java
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115 16 Pen_Ma
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116 ...
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117
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118 - Genotype table::
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119
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120 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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121 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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122 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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123 ...
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124
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125 - Coverage table::
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126
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127 chrM 0 G G 0 0 0 0 0 0 0 0 0 0 0 0 0
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128 chrM 1 T T 0 0 3 0 0 50 0 0 0 0 0 2 0
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129 chrM 2 T T 0 0 5 0 0 50 0 0 0 0 0 2 0
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130 ...
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131
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132 - Coverage threshold = 0
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133
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134 - Percentage of individuals = 0.0
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135
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136 - The output is::
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137
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138 4 19 15428
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139 W_Java GTTCATCATGTTCATCGAAT
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140 E_Java GTTCATCATGTTCATCGAAC
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141 Pen_Ma GTTCATCATGTTCATCGAAT
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142
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143 In a case were option genotype is selected with the inputs:
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144
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145 - Gene dataset table input::
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146
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147 1 ENSLAFT00000017123 chrM + 1002 1061 1002 1061 1 1002, 1061, 0 ENSLAFG00000017122 cmpl incmpl 0, BTRC ENSLAFT00000017123 ENSLAFP00000014355
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148 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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149 1 ENSLAFT00000008925 chrM + 990 1000 990 1000 1 990, 1000, 0 ENSLAFG00000008924 incmpl incmpl 0, PRKG1 ENSLAFT00000008925 ENSLAFP00000007492
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150 ...
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151
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152 In this table:
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153
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154 column with transcript start = 5
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155 column with transcript end = 6
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156 column with coding start = 7
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157 column with coding end = 8
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158 column with exon starts = 10
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159 column with exon ends = 11
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160
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161 - gd_indivs::
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162
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163 7 W_Java
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164 10 E_Java
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165 16 Pen_Ma
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166 ...
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167
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168 - Genotype table::
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169
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170 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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171 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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172 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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173 ...
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174
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175 The outputs are going to one file for each sequence in the input gene
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176 dataset table (as long as they are included in the input FASTA file).
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177 </help>
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178 </tool>