Mercurial > repos > tduigou > sbol_converter

annotate sbol_converter.xml @ 3:8d020045186c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
author tduigou
date Mon, 15 May 2023 01:30:26 +0000
parents 38a0feb2e79d
children 5814c9ffbdef
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
1 <tool id="sbol_converter" name="SBOL Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
0
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
2 <description>Convert between SBOL3 and other genetic design formats</description>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
3 <macros>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
5 <token name="@TOOL_VERSION@">1.0a16</token>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
6 </macros>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
7 <requirements>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
9 </requirements>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
11 #if str($convert_type.type) == "SBOL2 to SBOL3"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
12 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
13 sbol2to3 -o '$output' 'input.$sbol2_input.ext'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
14 #elif str($convert_type.type) == "SBOL3 to SBOL2"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
15 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
16 sbol3to2 -o '$output' 'input.$sbol3_input.ext'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
17 #elif str($convert_type.type) == "SBOL3 to GENBANK"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
18 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
19 sbol2genbank -o '$output' 'input.$sbol3_input.ext'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
20 #elif str($convert_type.type) == "GENBANK to SBOL3"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
21 ln -sv '$genbank_input' 'input.$genbank_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
22 genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
23 #elif str($convert_type.type) == "SBOL3 to FASTA"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
24 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
25 sbol2fasta -o '$output' 'input.$sbol3_input.ext'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
26 #elif str($convert_type.type) == "FASTA to SBOL3"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
27 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
28 fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
29 #elif str($convert_type.type) == "SBOL2 to FASTA"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
30 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
31 sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
32 #elif str($convert_type.type) == "FASTA to SBOL2"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
33 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
34 sbol-converter FASTA SBOL2 -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
35 #end if
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
36 ]]></command>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
37 <inputs>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
38 <conditional name="convert_type">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
39 <param name="type" type="select" label="Converting type" help="Choose the format (input/ouput) for SBOL conversion">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
40 <option value="SBOL2 to SBOL3" selected="True">From SBOL2 to SBOL3</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
41 <option value="SBOL2 to FASTA" >From SBOL2 to FASTA</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
42 <option value="SBOL3 to SBOL2" >From SBOL3 to SBOL2</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
43 <option value="SBOL3 to FASTA" >From SBOL3 to FASTA</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
44 <option value="SBOL3 to GENBANK" >From SBOL3 to GENBANK</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
45 <option value="GENBANK to SBOL3" >From GENBANK to SBOL3</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
46 <option value="FASTA to SBOL3" >From FASTA to SBOL3</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
47 <option value="FASTA to SBOL2" >From FASTA to SBOL2</option>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
48 </param>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
49 <when value="SBOL2 to SBOL3">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
50 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
51 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
52 <when value="SBOL3 to SBOL2">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
53 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
54 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
55 <when value="SBOL3 to GENBANK">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
56 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
57 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
58 <when value="GENBANK to SBOL3">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
59 <param name="genbank_input" type="data" format="gb" label="Genbank input" help="Genbank file in GB format"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
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" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
61 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
62 <when value="SBOL3 to FASTA">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
63 <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
64 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
65 <when value="FASTA to SBOL3">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
66 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
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" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
68 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
69 <when value="SBOL2 to FASTA">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
70 <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
71 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
72 <when value="FASTA to SBOL2">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
73 <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
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" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
75 </when>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
76 </conditional>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
77 </inputs>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
78 <outputs>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
79 <data name="output" format="nt" label="${tool.name} on ${on_string}: ${convert_type.type}" >
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
80 <change_format>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
81 <when input="convert_type.type" value="SBOL3 to GENBANK" format="gb" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
82 <when input="convert_type.type" value="SBOL3 to FASTA" format="fasta" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
83 <when input="convert_type.type" value="SBOL2 to FASTA" format="fasta" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
84 </change_format>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
85 </data>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
86 </outputs>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
87 <tests>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
88 <test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
89 <!-- test 1: check if identical outputs are produced sbol2 to sbol3-->
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
90 <conditional name="convert_type">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
91 <param name="type" value="SBOL2 to SBOL3"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
92 </conditional>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
93 <param name="sbol2_input" value="BASIC_construct_A1_sbol2_input.xml" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
94 <output name="output" file="BASIC_construct_A1_sbol3_output.nt" ftype="nt" compare="diff"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
95 </test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
96 <test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
97 <!-- test 2: check if identical outputs are produced sbol3 to genbank-->
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
98 <conditional name="convert_type">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
99 <param name="type" value="SBOL3 to GENBANK"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
100 </conditional>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
101 <param name="sbol3_input" value="BBa_J23101.nt" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
102 <output name="output" file="BBa_J23101.gb" ftype="gb" compare="diff"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
103 </test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
104
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
105 <test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
106 <!-- test 2: check if identical outputs are produced sbol3 to fasta-->
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
107 <conditional name="convert_type">
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
108 <param name="type" value="SBOL3 to FASTA"/>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
109 </conditional>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
110 <param name="sbol3_input" value="BBa_J23101.nt" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
111 <output name="output" >
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
112 <assert_contents>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
113 <has_text text=">BBa_J23101 constitutive promoter family member" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
114 <has_text text="tttacagctagctcagtcctaggtattatgctagc" />
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
115 </assert_contents>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
116 </output>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
117 </test>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
118 </tests>
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
119 <help><![CDATA[
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
120 SBOL Converter
3
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
121 ==============
0
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
122
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
123 Convert between SBOL3 and other genetic design formats.
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
124
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
125 Input
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
126 -----
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
127 Required:
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
128 * **INPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA input file.
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
129 * **Namespace URL**\ : Namespace URL, required for conversions from GenBank or from Fasta. Default=https://synbiohub.org/public/igem"
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
130
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
131 Output
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
132 ------
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
133 * **OUTPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA output file.
38a0feb2e79d planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents:
diff changeset
134 ]]></help>
3
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
135 <creator>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
136 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
137 </creator>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
138 <citations>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
139 <citation type="doi">10.1021/acssynbio.1c00188</citation>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
140 </citations>
8d020045186c planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eb4ce54a2a9e0cac18e737071a359d19f3af9a75
tduigou
parents: 0
diff changeset
141 </tool>