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planemo upload for repository https://github.com/ncbi/egapx commit 9e59da535540cb4d5c1c412bb2b0969744dfb0b0-dirty
author fubar
date Sun, 04 Aug 2024 02:30:36 +0000
parents d9c5c5b87fec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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1 #!/usr/bin/env nextflow
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2 nextflow.enable.dsl=2
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3
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5 // Analog of shlex.split
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6 def List<String> shellSplit(CharSequence s) {
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7 List<String> tokens = []
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8 boolean escaping = false
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9 char quoteChar = ' '
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10 boolean quoting = false
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11 int lastCloseQuoteIndex = Integer.MIN_VALUE
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12 StringBuilder current = new StringBuilder()
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13
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14 s.eachWithIndex { c, i ->
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15 if (escaping) {
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16 current.append(c)
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17 escaping = false
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18 // } else if (c == '\\' && !(quoting && quoteChar == '\'')) {
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19 } else if (c == '\\' && !quoting) {
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20 escaping = true
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21 } else if (quoting && c == quoteChar) {
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22 quoting = false
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23 lastCloseQuoteIndex = i
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24 } else if (!quoting && (c == '\'' || c == '"')) {
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25 quoting = true
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26 quoteChar = c
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27 } else if (!quoting && c.isAllWhitespace()) {
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28 if (current.size() > 0 || lastCloseQuoteIndex == (i - 1)) {
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29 tokens.add(current.toString())
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30 current = new StringBuilder()
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31 }
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32 } else {
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33 current.append(c)
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34 }
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35 }
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36 if (current.size() > 0 || lastCloseQuoteIndex == (s.length() - 1)) {
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37 tokens.add(current.toString())
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38 }
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39
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40 return tokens
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41 }
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42
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43
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44 // Convert a parameter list into a map
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45 def Map<String, String> to_map(List<String> list )
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46 {
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47 def map = [:]
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48 def s = list.size()
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49 def i = 0
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50 while (i < s)
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51 {
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52 def elem = list.get(i)
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53 i = i + 1
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54 if (elem.size() > 0 && elem[0] == '-')
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55 {
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56 if (i < s) {
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57 def val = list.get(i)
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58 if ( val.size() > 0 && (val[0] != '-' || val.contains(' ')) )
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59 {
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60 map[elem] = val
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61 i = i + 1
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62 } else {
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63 map[elem] = ""
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64 }
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65 } else {
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66 map[elem] = ""
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67 }
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68 } else {
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69 println("Error: parameter string not well formed, map ${map}, elem ${elem}, i ${i}, s ${s}")
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70 return map
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71 }
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72 }
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73 return map
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74 }
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75
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76
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77 def quote(String s)
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78 {
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79 if (s.size() > 0 && !(s =~ /[^\w@%+=:,.\/-]/)) {
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80 return s
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81 }
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82 return "'" + s + "'"
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83 }
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84
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85
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86 // Read a section of the parameters and merge them into the default parameters
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87 // Parameters:
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88 // default_params: the default parameters, string
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89 // parameters: the parameters as a map from string to string
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90 // section_name: the name of the section in the parameters map to use
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91 // Return: the merged parameters
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92 def merge_params(default_params, parameters, section_name)
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93 {
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94 def section = parameters.get(section_name, "")
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95 def update_map = to_map(shellSplit(section))
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96 def default_params_map = to_map(shellSplit(default_params))
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97 default_params_map.putAll(update_map)
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98 def l = []
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99 default_params_map.each { parameter, value ->
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100 l << quote(parameter)
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101 if (value.size() > 0) {
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102 l << quote(value)
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103 }
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104 }
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105
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106 return l.join(" ")
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107 }
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108
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109
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110
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111 process clean_fasta_ids {
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112 input:
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113 path fasta_in
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114 output:
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115 path "fasta_out", emit: 'fasta_out'
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116 script:
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117 """
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118 ## turns Fasta inputs formatted with multi-part IDs into
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119 ## single-part IDs, like
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120 ## >gi|1234|ref|NW_1234.1 Some Defline For This Org
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121 ## >gi|1234 Some Defline For This Org
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122 ## LDS chokes on the multi-part IDs.
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123 # the base64 nonsense is because I couldnt get it to not complain about the regex as syntax errors in some way.
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124 # its just this:
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125 # import re,sys;
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126 # for l in sys.stdin:
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127 # <I had to delete the regex here because even in a comment nextflow lost it>
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128 echo 'aW1wb3J0IHJlLHN5czsKZm9yIGwgaW4gc3lzLnN0ZGluOgogICAgcHJpbnQocmUuc3ViKHIiXig+' > reol.b64
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129 echo 'Z2lcfFxkKylcfD8oW2Etel0rXHxbQS1aX10rW1xkXC5dK1x8KSguKikiLCAiXGc8MT5cZzwzPiIs' >> reol.b64
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130 echo 'IGwuc3RyaXAoKSkpCg==' >> reol.b64
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131 base64 -d ./reol.b64 > ./reol.py
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132 cat ${fasta_in} | python reol.py > ./fasta_out
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133 """
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134 stub:
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135 """
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136 touch ./fasta.out
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137 """
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138 }
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139
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140
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141
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142 process multireader {
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143 input:
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144 path fasta_file
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145 val parameters
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146 output:
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147 path ('output/fasta_file.asnt') , emit: 'multireader_file'
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148 script:
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149 """
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150 mkdir -p output
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151 if [ -n "$fasta_file" ]; then
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152 multireader $parameters -out-format asn_text -input $fasta_file -output output/fasta_file.asnt
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153 else
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154 touch output/fasta_file.asnt
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155 fi
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156 """
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157 stub:
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158 """
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159 mkdir -p output
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160 touch output/fasta_file.asnt
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161 """
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162 }