Mercurial > repos > tduigou > sbol_converter

annotate sbol_converter.xml @ 1:529ee7dc1be9 draft

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author tduigou
date Tue, 18 Apr 2023 07:51:41 +0000
parents 38a0feb2e79d
children 8d020045186c
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1 <tool id="sbol_converter" name="SBOL Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Convert between SBOL3 and other genetic design formats</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">1.0a16</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if str($convert_type.type) == "SBOL2 to SBOL3"
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12 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
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13 sbol2to3 -o '$output' 'input.$sbol2_input.ext'
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14 #elif str($convert_type.type) == "SBOL3 to SBOL2"
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15 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
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16 sbol3to2 -o '$output' 'input.$sbol3_input.ext'
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17 #elif str($convert_type.type) == "SBOL3 to GENBANK"
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18 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
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19 sbol2genbank -o '$output' 'input.$sbol3_input.ext'
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20 #elif str($convert_type.type) == "GENBANK to SBOL3"
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21 ln -sv '$genbank_input' 'input.$genbank_input.ext' &&
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22 genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
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23 #elif str($convert_type.type) == "SBOL3 to FASTA"
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24 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
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25 sbol2fasta -o '$output' 'input.$sbol3_input.ext'
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26 #elif str($convert_type.type) == "FASTA to SBOL3"
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27 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
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28 fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
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29 #elif str($convert_type.type) == "SBOL2 to FASTA"
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30 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
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31 sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext'
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32 #elif str($convert_type.type) == "FASTA to SBOL2"
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33 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
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34 sbol-converter FASTA SBOL2 -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
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35 #end if
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36 ]]></command>
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37 <inputs>
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38 <conditional name="convert_type">
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39 <param name="type" type="select" label="Converting type" help="Choose the format (input/ouput) for SBOL conversion">
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40 <option value="SBOL2 to SBOL3" selected="True">From SBOL2 to SBOL3</option>
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41 <option value="SBOL2 to FASTA" >From SBOL2 to FASTA</option>
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42 <option value="SBOL3 to SBOL2" >From SBOL3 to SBOL2</option>
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43 <option value="SBOL3 to FASTA" >From SBOL3 to FASTA</option>
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44 <option value="SBOL3 to GENBANK" >From SBOL3 to GENBANK</option>
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45 <option value="GENBANK to SBOL3" >From GENBANK to SBOL3</option>
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46 <option value="FASTA to SBOL3" >From FASTA to SBOL3</option>
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47 <option value="FASTA to SBOL2" >From FASTA to SBOL2</option>
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48 </param>
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49 <when value="SBOL2 to SBOL3">
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50 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format"/>
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51 </when>
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52 <when value="SBOL3 to SBOL2">
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53 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
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54 </when>
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55 <when value="SBOL3 to GENBANK">
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56 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
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57 </when>
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58 <when value="GENBANK to SBOL3">
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59 <param name="genbank_input" type="data" format="gb" label="Genbank input" help="Genbank file in GB format"/>
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60 <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from GenBank. Default=https://synbiohub.org/public/igem" />
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61 </when>
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62 <when value="SBOL3 to FASTA">
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63 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
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64 </when>
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65 <when value="FASTA to SBOL3">
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66 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
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67 <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" />
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68 </when>
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69 <when value="SBOL2 to FASTA">
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70 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format" />
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71 </when>
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72 <when value="FASTA to SBOL2">
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73 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
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74 <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" />
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75 </when>
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76 </conditional>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="nt" label="${tool.name} on ${on_string}: ${convert_type.type}" >
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80 <change_format>
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81 <when input="convert_type.type" value="SBOL3 to GENBANK" format="gb" />
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82 <when input="convert_type.type" value="SBOL3 to FASTA" format="fasta" />
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83 <when input="convert_type.type" value="SBOL2 to FASTA" format="fasta" />
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84 </change_format>
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85 </data>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <!-- test 1: check if identical outputs are produced sbol2 to sbol3-->
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90 <conditional name="convert_type">
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91 <param name="type" value="SBOL2 to SBOL3"/>
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92 </conditional>
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93 <param name="sbol2_input" value="BASIC_construct_A1_sbol2_input.xml" />
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94 <output name="output" file="BASIC_construct_A1_sbol3_output.nt" ftype="nt" compare="diff"/>
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95 </test>
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96
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97 <test>
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98 <!-- test 2: check if identical outputs are produced sbol3 to genbank-->
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99 <conditional name="convert_type">
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100 <param name="type" value="SBOL3 to GENBANK"/>
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101 </conditional>
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102 <param name="sbol3_input" value="BBa_J23101.nt" />
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103 <output name="output" file="BBa_J23101.gb" ftype="gb" compare="diff"/>
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104 </test>
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105
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106 <test>
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107 <!-- test 2: check if identical outputs are produced sbol3 to fasta-->
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108 <conditional name="convert_type">
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109 <param name="type" value="SBOL3 to FASTA"/>
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110 </conditional>
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111 <param name="sbol3_input" value="BBa_J23101.nt" />
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112 <output name="output" >
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113 <assert_contents>
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114 <has_text text=">BBa_J23101 constitutive promoter family member" />
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115 <has_text text="tttacagctagctcagtcctaggtattatgctagc" />
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116 </assert_contents>
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117 </output>
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118 </test>
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119 </tests>
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120 <help><![CDATA[
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121 SBOL Converter
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122 ================
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123
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124 Convert between SBOL3 and other genetic design formats.
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125
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126 Input
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127 -----
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128 Required:
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129 * **INPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA input file.
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130 * **Namespace URL**\ : Namespace URL, required for conversions from GenBank or from Fasta. Default=https://synbiohub.org/public/igem"
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131
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132 Output
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133 ------
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134 * **OUTPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA output file.
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135
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136 Project Links
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137 ------------------
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138 * `GitHub <https://github.com/SynBioDex/SBOL-utilities>`_
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139
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140 License
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141 -------
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142 * `MIT <https://github.com/SynBioDex/SBOL-utilities/blob/develop/LICENSE.txt>`_
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143 ]]></help>
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144 </tool>