Mercurial > repos > tduigou > sbol_converter
comparison sbol_converter.xml @ 0:38a0feb2e79d draft
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author | tduigou |
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date | Thu, 15 Sep 2022 13:40:15 +0000 |
parents | |
children | 8d020045186c |
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1 <tool id="sbol_converter" name="SBOL Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> | |
2 <description>Convert between SBOL3 and other genetic design formats</description> | |
3 <macros> | |
4 <token name="@VERSION_SUFFIX@">0</token> | |
5 <token name="@TOOL_VERSION@">1.0a16</token> | |
6 </macros> | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement> | |
9 </requirements> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 #if str($convert_type.type) == "SBOL2 to SBOL3" | |
12 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && | |
13 sbol2to3 -o '$output' 'input.$sbol2_input.ext' | |
14 #elif str($convert_type.type) == "SBOL3 to SBOL2" | |
15 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && | |
16 sbol3to2 -o '$output' 'input.$sbol3_input.ext' | |
17 #elif str($convert_type.type) == "SBOL3 to GENBANK" | |
18 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && | |
19 sbol2genbank -o '$output' 'input.$sbol3_input.ext' | |
20 #elif str($convert_type.type) == "GENBANK to SBOL3" | |
21 ln -sv '$genbank_input' 'input.$genbank_input.ext' && | |
22 genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace' | |
23 #elif str($convert_type.type) == "SBOL3 to FASTA" | |
24 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && | |
25 sbol2fasta -o '$output' 'input.$sbol3_input.ext' | |
26 #elif str($convert_type.type) == "FASTA to SBOL3" | |
27 ln -sv '$fasta_input' 'input.$fasta_input.ext' && | |
28 fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace' | |
29 #elif str($convert_type.type) == "SBOL2 to FASTA" | |
30 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && | |
31 sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext' | |
32 #elif str($convert_type.type) == "FASTA to SBOL2" | |
33 ln -sv '$fasta_input' 'input.$fasta_input.ext' && | |
34 sbol-converter FASTA SBOL2 -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace' | |
35 #end if | |
36 ]]></command> | |
37 <inputs> | |
38 <conditional name="convert_type"> | |
39 <param name="type" type="select" label="Converting type" help="Choose the format (input/ouput) for SBOL conversion"> | |
40 <option value="SBOL2 to SBOL3" selected="True">From SBOL2 to SBOL3</option> | |
41 <option value="SBOL2 to FASTA" >From SBOL2 to FASTA</option> | |
42 <option value="SBOL3 to SBOL2" >From SBOL3 to SBOL2</option> | |
43 <option value="SBOL3 to FASTA" >From SBOL3 to FASTA</option> | |
44 <option value="SBOL3 to GENBANK" >From SBOL3 to GENBANK</option> | |
45 <option value="GENBANK to SBOL3" >From GENBANK to SBOL3</option> | |
46 <option value="FASTA to SBOL3" >From FASTA to SBOL3</option> | |
47 <option value="FASTA to SBOL2" >From FASTA to SBOL2</option> | |
48 </param> | |
49 <when value="SBOL2 to SBOL3"> | |
50 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format"/> | |
51 </when> | |
52 <when value="SBOL3 to SBOL2"> | |
53 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> | |
54 </when> | |
55 <when value="SBOL3 to GENBANK"> | |
56 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> | |
57 </when> | |
58 <when value="GENBANK to SBOL3"> | |
59 <param name="genbank_input" type="data" format="gb" label="Genbank input" help="Genbank file in GB format"/> | |
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" /> | |
61 </when> | |
62 <when value="SBOL3 to FASTA"> | |
63 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> | |
64 </when> | |
65 <when value="FASTA to SBOL3"> | |
66 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/> | |
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" /> | |
68 </when> | |
69 <when value="SBOL2 to FASTA"> | |
70 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format" /> | |
71 </when> | |
72 <when value="FASTA to SBOL2"> | |
73 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/> | |
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" /> | |
75 </when> | |
76 </conditional> | |
77 </inputs> | |
78 <outputs> | |
79 <data name="output" format="nt" label="${tool.name} on ${on_string}: ${convert_type.type}" > | |
80 <change_format> | |
81 <when input="convert_type.type" value="SBOL3 to GENBANK" format="gb" /> | |
82 <when input="convert_type.type" value="SBOL3 to FASTA" format="fasta" /> | |
83 <when input="convert_type.type" value="SBOL2 to FASTA" format="fasta" /> | |
84 </change_format> | |
85 </data> | |
86 </outputs> | |
87 <tests> | |
88 <test> | |
89 <!-- test 1: check if identical outputs are produced sbol2 to sbol3--> | |
90 <conditional name="convert_type"> | |
91 <param name="type" value="SBOL2 to SBOL3"/> | |
92 </conditional> | |
93 <param name="sbol2_input" value="BASIC_construct_A1_sbol2_input.xml" /> | |
94 <output name="output" file="BASIC_construct_A1_sbol3_output.nt" ftype="nt" compare="diff"/> | |
95 </test> | |
96 | |
97 <test> | |
98 <!-- test 2: check if identical outputs are produced sbol3 to genbank--> | |
99 <conditional name="convert_type"> | |
100 <param name="type" value="SBOL3 to GENBANK"/> | |
101 </conditional> | |
102 <param name="sbol3_input" value="BBa_J23101.nt" /> | |
103 <output name="output" file="BBa_J23101.gb" ftype="gb" compare="diff"/> | |
104 </test> | |
105 | |
106 <test> | |
107 <!-- test 2: check if identical outputs are produced sbol3 to fasta--> | |
108 <conditional name="convert_type"> | |
109 <param name="type" value="SBOL3 to FASTA"/> | |
110 </conditional> | |
111 <param name="sbol3_input" value="BBa_J23101.nt" /> | |
112 <output name="output" > | |
113 <assert_contents> | |
114 <has_text text=">BBa_J23101 constitutive promoter family member" /> | |
115 <has_text text="tttacagctagctcagtcctaggtattatgctagc" /> | |
116 </assert_contents> | |
117 </output> | |
118 </test> | |
119 </tests> | |
120 <help><![CDATA[ | |
121 SBOL Converter | |
122 ================ | |
123 | |
124 Convert between SBOL3 and other genetic design formats. | |
125 | |
126 Input | |
127 ----- | |
128 Required: | |
129 * **INPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA input file. | |
130 * **Namespace URL**\ : Namespace URL, required for conversions from GenBank or from Fasta. Default=https://synbiohub.org/public/igem" | |
131 | |
132 Output | |
133 ------ | |
134 * **OUTPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA output file. | |
135 | |
136 Project Links | |
137 ------------------ | |
138 * `GitHub <https://github.com/SynBioDex/SBOL-utilities>`_ | |
139 | |
140 License | |
141 ------- | |
142 * `MIT <https://github.com/SynBioDex/SBOL-utilities/blob/develop/LICENSE.txt>`_ | |
143 ]]></help> | |
144 </tool> |