Mercurial > repos > bebatut > convert_extract_sequence_file

annotate convert_extract_sequence_file.xml @ 0:01c2b74b3a21 draft

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author bebatut
date Tue, 26 Apr 2016 08:18:18 -0400
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children 158642ce204f
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1 <tool id="convert_extract_sequence_file" name="Convert/ Extract information" version="1.0.0">
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2
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3 <description>from a sequence file, with possible constraints</description>
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4
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5 <macros>
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6 <xml name="extraction_option">
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7 <param name="to_extract" type="select" display="checkboxes" multiple="true" label="Information to extract" help="">
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8 <option value="id">Identifiant</option>
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9 <option value="length">Length</option>
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10 <validator type="no_options" message="Select at least one information to extract"/>
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11 </param>
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12 </xml>
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13
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14 <xml name="extraction_test">
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15 <param name='specific_extraction' type="select" label="Extract specific information?" help="If no is selected, a sequence file is generated. If yes, a text file containing the wanted information is generated">
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16 <option value="True">Yes</option>
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17 <option value="False" selected="true">No</option>
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18 </param>
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19 </xml>
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20 </macros>
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21
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22 <requirements>
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23 </requirements>
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24
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25 <stdio>
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26 </stdio>
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27
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28 <version_command>
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29 </version_command>
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30
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31 <!--<command>-->
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32 <command><![CDATA[
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33 python $__tool_directory__/convert_extract_sequence_file.py
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34 --input $sequence_file_format.sequence_file
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35
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36 --custom_extraction_type $sequence_file_format.extraction.specific_extraction
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37
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38 #if $sequence_file_format.extraction.specific_extraction == "True":
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39 --to_extract "{$sequence_file_format.extraction.to_extract}"
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40 --output_information $information_file
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41 #else if $sequence_file_format.format=="fastq":
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42 --split $sequence_file_format.extraction.split.split_test
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43 #if $sequence_file_format.extraction.split.split_test :
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44 --quality_format $sequence_file_format.extraction.split.quality_format
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45 --output_sequence $fasta_sequence_file_from_fastq
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46 --output_quality $quality_file
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47 #else:
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48 --output_sequence $fastq_sequence_file
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49 #end if
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50 #else:
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51 --output_sequence $fasta_sequence_file
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52 #end if
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53
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54 #if $constraints.constrained_extraction == "True" :
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55 #for $i, $constrain in enumerate( $constraints.constraint_definition )
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56 #set info_to_constrain=$constrain.constrained_information['info_to_constrain']
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57 #if $info_to_constrain in ("id"):
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58 --constraint "$info_to_constrain:
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59 ${constrain.constrained_information.constraint_type.type}:
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60 ${constrain.constrained_information.constraint_type.value}"
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61 #else:
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62 #for $j, $sub_constrain in enumerate( $constrain.constrained_information.constraint_definition )
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63 --constraint "$info_to_constrain:
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64 ${sub_constrain.type}:
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65 ${sub_constrain.value}"
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66 #end for
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67 #end if
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68 #end for
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69 #end if
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70
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71 --report $report_filepath
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72 --format $sequence_file_format.format
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73 ]]>
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74 </command>
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75
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76 <inputs>
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77 <conditional name="sequence_file_format">
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78 <param name="format" type="select" display="radio"
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79 label="Format of the sequence file" help="">
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80 <option value="fasta">Fasta</option>
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81 <option value="fastq">FastQ</option>
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82 </param>
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83 <when value="fastq">
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84 <param name="sequence_file" type="data" format="fastq"
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85 label="Sequence file" help=""/>
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86 <conditional name="extraction">
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87 <expand macro="extraction_test"/>
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88
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89 <when value="True">
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90 <expand macro="extraction_option"/>
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91 </when>
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92 <when value="False">
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93 <conditional name="split">
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94 <param name='split_test' type="select" label="Split file into sequence and quality files?" help="If yes is selected, a fasta and a quality file are generated. If no, a fastq file is generated">
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95 <option value="True" selected="true">Yes</option>
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96 <option value="False">No</option>
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97 </param>
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98
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99 <when value="True">
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100 <param name="quality_format" type="select" display="radio" label="Coding of quality scores?" help="">
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101 <option value="sanger" selected="true">Sanger (Phred+33)</option>
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102 <option value="solexa">Solexa (Solexa+64) </option>
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103 <option value="illumina_1_3">Illumina 1.3+ (Phred+64) </option>
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104 <option value="illumina_1_5">Illumina 1.5+ (Phred+64) </option>
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105 <option value="illumina_1_8">Illumina 1.8+ (Phred+33) </option>
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106 </param>
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107 </when>
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108 <when value="False" />
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109 </conditional>
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110 </when>
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111 </conditional>
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112 </when>
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113
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114 <when value="fasta">
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115 <param name="sequence_file" type="data" format="fasta"
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116 label="Sequence file" help=""/>
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117 <conditional name="extraction">
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118 <expand macro="extraction_test"/>
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119
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120 <when value="True">
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121 <expand macro="extraction_option"/>
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122 </when>
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123 <when value="False" />
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124 </conditional>
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125 </when>
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126 </conditional>
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127
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128 <conditional name="constraints">
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129 <param name='constrained_extraction' type='select' label="Constrain extraction?" help="">
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130 <option value="True">Yes</option>
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131 <option value="False" selected="true">No</option>
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132 </param>
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133
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134 <when value="True">
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135 <repeat name="constraint_definition" title="Constraints on sequences" min="1">
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136 <conditional name="constrained_information">
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137 <param name="info_to_constrain" type="select" label="Information to constrain" help="">
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138 <option value="id">Identifiant</option>
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139 <option value="length">Length</option>
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140 </param>
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141 <when value="id">
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142 <conditional name="constraint_type">
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143 <param name="type" type="select" display="radio" label="Type of constraint" help="">
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144 <option value="equal">Equal a value</option>
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145 <option value="in">In a list</option>
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146 <option value="not_in">Not in a list</option>
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147 </param>
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148 <when value="equal">
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149 <param name="value" type="text" size="200" label="Equal to" help=""/>
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150 <validator type="empty_field" message="Give a value"/>
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151 </when>
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152 <when value="in">
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153 <param format="txt" name="value" type="data" label="List of constraint" help="Text file with a value per line and nothing else"/>
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154 <validator type="unspecified_build" message="Select a file"/>
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155 </when>
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156 <when value="not_in">
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157 <param format="txt" name="value" type="data" label="List of constraint" help="Text file with a value per line and nothing else"/>
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158 <validator type="unspecified_build" message="Select a file"/>
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159 </when>
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160 </conditional>
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161 </when>
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162 <when value="length">
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163 <repeat name="constraint_definition" title="Constraint on sequence length" min="1">
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164 <param name="type" type="select" label="Type of constraint" help="">
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165 <option value="equal">Equal to </option>
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166 <option value="lower">Lower than </option>
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167 <option value="strictly_lower">Strictly lower than </option>
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168 <option value="greater">Greater than </option>
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169 <option value="strictly_greater">Strictly greater than </option>
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170 </param>
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171 <param name="value" type="integer" min="0" max="3000" value="100" label="Value" help=""/>
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172 </repeat>
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173 </when>
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174 </conditional>
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175 </repeat>
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176 </when>
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177 <when value="False" />
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178 </conditional> />
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179 </inputs>
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180
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181 <outputs>
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182 <data format="txt" name="information_file"
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183 label="${tool.name} on ${on_string}: Information">
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184 <filter>((sequence_file_format['extraction']['specific_extraction'] == "True" ))</filter>
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185 </data>
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186
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187 <data format="fasta" name="fasta_sequence_file"
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188 label="${tool.name} on ${on_string}: Extracted sequences" >
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189 <filter>((sequence_file_format['format'] == 'fasta' and not sequence_file_format['extraction']['specific_extraction']== "True" ))</filter>
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190 </data>
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191
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192 <data format="fastq" name="fastq_sequence_file"
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193 label="${tool.name} on ${on_string}: Extracted sequences">
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194 <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "False" ))</filter>
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195 </data>
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196
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197 <data format="qual" name="quality_file"
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198 label="${tool.name} on ${on_string}: Extracted quality">
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199 <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "True" ))</filter>
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200 </data>
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201
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202 <data format="fasta" name="fasta_sequence_file_from_fastq"
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203 label="${tool.name} on ${on_string}: Extracted sequences">
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204 <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "True" ))</filter>
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205 </data>
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206
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207 <data format="txt" name="report_filepath"
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208 label="${tool.name} on ${on_string}: Report"/>
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209 </outputs>
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210
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211 <tests>
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212 <test>
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213 <param name="format" value="fasta"/>
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214 <param name="sequence_file" value="input_sequence_file.fasta"/>
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215 <param name="specific_extraction" value="True" />
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216 <param name="to_extract" value="length" />
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217 <param name="constrained_extraction" value="False" />
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218 <output name="information_file" file="information_lenght_fasta_output.txt"/>
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219 <output name="report_filepath" file="report_length_fasta_output.txt"/>
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220 </test>
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221 <test>
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222 <param name="format" value="fastq"/>
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223 <param name="sequence_file" value="input_sequence_file.fastq"/>
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224 <param name="specific_extraction" value="False" />
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225 <param name="split_test" value="True" />
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226 <param name="quality_format" value="illumina_1_3" />
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227 <param name="constrained_extraction" value="False" />
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228 <output name="quality_file" file="extracted_quality_illumina_1_3_fastq_output.qual"/>
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229 <output name="fasta_sequence_file_from_fastq" file="extracted_sequences_illumina_1_3_fastq_output.fasta"/>
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230 <output name="report_filepath" file="report_illumina_1_3_fastq_output.txt"/>
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231 </test>
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232 </tests>
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233
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234 <help><![CDATA[
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235
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236 **What it does**
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237
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238 This tool extracts information (sequences, id, length, ...) from sequence files or convert a FastQ file to Fasta file.
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239
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240 Some constraints could be added to extraction/conversion. For example, only sequences with more than 30 bp could be extracted. Or, a sequences whose the identifiant is in a list.
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241
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242 The input is a sequence file in fasta or fastq format. The tool generates different outputs given the chosen parameters.
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243 ]]>
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244 </help>
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245
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246 <citations>
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247 </citations>
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248 </tool>
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249