Mercurial > repos > iuc > optdoe

annotate optdoe.xml @ 1:9a2fb8d83eb0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
author iuc
date Fri, 10 Feb 2023 15:04:50 +0000
parents 4f1acbf17618
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
1 <tool id="optdoe" name="Optimal Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
2 <description>Combine selected genetic parts and enzyme variants for the desired pathways</description>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
3 <macros>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
1
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
5 <token name="@TOOL_VERSION@">v2.0.2</token>
0
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
6 </macros>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
7 <requirements>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">doebase</requirement>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
9 </requirements>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
11 python -m doebase
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
12 --func doeGetSBOL
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
13 #if $adv.genes_sbol_file
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
14 --sbol_file '$adv.genes_sbol_file'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
15 #end if
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
16 #if $adv.ref_parts_file
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
17 --ref_parts_file '$adv.ref_parts_file'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
18 #end if
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
19 --libsize '$adv.libsize'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
20 $adv.get_sequences
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
21 $adv.backtranslate
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
22 --codon_table '$adv.codon_table'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
23 '$genes_file'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
24 '$constructs'
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
25 ]]></command>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
26 <inputs>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
27 <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
28 <section name="adv" title="Advanced Options" expanded="false">
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
29 <param name="genes_sbol_file" type="data" format="xml" optional="true" label="Optimised Genes" help="SBOL file with genes associated with different RBS. Provided by the tool PartsGenie"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
30 <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
31 <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
32 <param argument="--get_sequences" type="boolean" truevalue="--get_sequences true" falsevalue="--get_sequences false" checked="true" label="Get sequences" help="Grab the sequence for each part of the SBOL output"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
33 <param argument="--backtranslate" type="boolean" truevalue="--backtranslate true" falsevalue="--backtranslate false" checked="true" label="Back translate" help="Translate the protein sequence given by its Uniprot ID to a DNA sequence"/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
34 <param argument="--codon_table" type="select" label="Codon Table">
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
35 <option value="Eecoli.cut">Escherichia coli K12</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
36 <option value="Ehuman.cut">Homo sapiens</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
37 <option value="Eacica.cut">Acinetobacter calcoaceticus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
38 <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
39 <option value="Eanasp.cut">Anabaena sp</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
40 <option value="Earath.cut">Arabidopsis thaliana</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
41 <option value="Eazovi.cut">Azotobacter vinelandii</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
42 <option value="Ebacme.cut">Bacillus megaterium</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
43 <option value="Ebacst.cut">Geobacillus stearothermophilus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
44 <option value="Ebacsu.cut">Bacillus subtilis</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
45 <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
46 <option value="Ebommo.cut">Bombyx mori (silkmoth)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
47 <option value="Ebovin.cut">Bos taurus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
48 <option value="Ebpphx.cut">Bacteriophage phi-X174</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
49 <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
50 <option value="Ebrana.cut">Brassica napus (rape)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
51 <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
52 <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
53 <option value="Ecanal.cut">Candida albicans</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
54 <option value="Ecanfa.cut">Canis familiaris (dog)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
55 <option value="Ecaucr.cut">Caulobacter crescentus CB15</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
56 <option value="Echick.cut">Gallus gallus (chicken)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
57 <option value="Echlre.cut">Chlamydomonas reinhardtii</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
58 <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
59 <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
60 <option value="Ecrigr.cut">Cricetulus greseus (hamster)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
61 <option value="Ecyapa.cut">Cyanophora paradoxa</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
62 <option value="Edicdi.cut">Dictyostelium discoideum</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
63 <option value="Edicdi_high.cut">Dictyostelium discoideum (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
64 <option value="Edrome.cut">Drosophila melanogaster</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
65 <option value="Edrome_high.cut">Drosophila melanogaster (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
66 <option value="Eecoli_high.cut">Escherichia coli K12 (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
67 <option value="Eemeni.cut">Emericella nidulans</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
68 <option value="Eemeni_mit.cut">Emericella nidulans mitochondrion</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
69 <option value="Eemeni_high.cut">Emericella nidulans highly expressed</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
70 <option value="Eerwct.cut">Erwinia carotovora subsp atroseptica SCRI1043</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
71 <option value="Ehaein.cut">Haemophilus influenzae Rd KW20</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
72 <option value="Ehalma.cut">Haloarcula marismortui ATCC 43049 (Halobacterium marismortui)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
73 <option value="Ehalsa.cut">Halobacterium salinarum NRC-1 (Halobacterium halobium)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
74 <option value="Ehorvu.cut">Hordeum vulgare subsp vulgare (Barley)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
75 <option value="Eklepn.cut">Klebsiella pneumoniae</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
76 <option value="Eklula.cut">Kluyveromyces lactis NRRL Y-1140</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
77 <option value="Elacdl.cut">Lactococcus lactis subsp lactis Il1403 L. delbrueckii subsp lactis</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
78 <option value="Elyces.cut">Lycopersicon esculentum (tomato)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
79 <option value="Emacfa.cut">Macaca fascicularis</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
80 <option value="Emaize.cut">Zea mays</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
81 <option value="Emaize_chl.cut">Zea mays chloroplast</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
82 <option value="Emammal_high.cut">Mammalian species (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
83 <option value="Emanse.cut">Manduca sexta</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
84 <option value="Emarpo_chl.cut">Marchantia polymorpha chloroplast (liverwort)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
85 <option value="Emedsa.cut">Medicago sativa</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
86 <option value="Emetth.cut">Methanothermobacter thermautotrophicus str Delta H</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
87 <option value="Emouse.cut">Mus musculus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
88 <option value="Emyctu.cut">Mycobacterium tuberculosis H37Rv</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
89 <option value="Eneigo.cut">Neisseria gonorrhoeae</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
90 <option value="Eneucr.cut">Neurospora crassa</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
91 <option value="Eoncmy.cut">Oncorhynchus mykiss (rainbow trout)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
92 <option value="Eorysa.cut">Oryza sativa (rice)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
93 <option value="Eorysa_chl.cut">Oryza sativa chloroplast (rice)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
94 <option value="Epea.cut">Pisum sativum (pea)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
95 <option value="Epethy.cut">Petunia x hybrida</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
96 <option value="Ephavu.cut">Phaseolus vulgaris</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
97 <option value="Epig.cut">Sus scrofa (pig)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
98 <option value="Eplafa.cut">Plasmodium falciparum 3D7</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
99 <option value="Eprovu.cut">Proteus vulgaris</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
100 <option value="Epseae.cut">Pseudomonas aeruginosa PAO1</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
101 <option value="Epsepu.cut">Pseudomonas putida KT2440</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
102 <option value="Epsesm.cut">Pseudomonas syringae pv tomato str DC3000</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
103 <option value="Erabit.cut">Oryctolagus cuniculus (rabbit)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
104 <option value="Erat.cut">Rattus norvegicus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
105 <option value="Erhile.cut">Rhizobium leguminosarum</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
106 <option value="Erhime.cut">Sinorhizobium meliloti 1021</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
107 <option value="Erhoca.cut">Rhodobacter capsulatus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
108 <option value="Erhosh.cut">Rhodobacter sphaeroides</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
109 <option value="Esalsa.cut">Salmo salar (Atlantic salmon)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
110 <option value="Esalty.cut">Salmonella typhimurium LT2</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
111 <option value="Eschma.cut">Schistosoma mansoni</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
112 <option value="Eschpo.cut">Schizosaccharomyces pombe</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
113 <option value="Eschpo_cai.cut">Schizosaccharomyces pombe (CAI equivalent)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
114 <option value="Eschpo_high.cut">Schizosaccharomyces pombe (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
115 <option value="Eserma.cut">Serratia marcescens</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
116 <option value="Esheep.cut">Ovis aries (sheep)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
117 <option value="Esoltu.cut">Solanum tuberosum (potato)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
118 <option value="Esoybn.cut">Glycine max (soybean)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
119 <option value="Espiol.cut">Spinacia oleracea (spinach)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
120 <option value="Estaau.cut">Staphylococcus aureus</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
121 <option value="Estrco.cut">Streptomyces coelicolor A3 2</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
122 <option value="Estrmu.cut">Streptococcus mutans UA159</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
123 <option value="Estrpn.cut">Streptococcus pneumoniae R6</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
124 <option value="Estrpu.cut">Strongylocentrotus purpuratus (sea urchin)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
125 <option value="Esv40.cut">Simian Virus 40</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
126 <option value="Esynco.cut">Synechococcus sp WH 8102</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
127 <option value="Esyncy.cut">Synechocystis sp PCC 6803</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
128 <option value="Etetth.cut">Tetrahymena thermophila</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
129 <option value="Etheth.cut">Thermus thermophilus HB8</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
130 <option value="Etobac.cut">Nicotiana tabacum (tobacco)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
131 <option value="Etobac_chl.cut">Nicotiana tabacum chloroplast (tobacco)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
132 <option value="Etrybr.cut">Trypanosoma brucei</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
133 <option value="Etrycr.cut">Trypanosoma cruzi</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
134 <option value="Evibch.cut">Vibrio cholerae O1 biovar eltor str N16961</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
135 <option value="Ewheat.cut">Triticum aestivum (wheat)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
136 <option value="Exenla.cut">Xenopus laevis</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
137 <option value="Eyeast.cut">Saccharomyces cerevisiae</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
138 <option value="Eyeast_cai.cut">Saccharomyces cerevisiae original CAI set</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
139 <option value="Eyeast_high.cut">Saccharomyces cerevisiae (high)</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
140 <option value="Eyeast_mit.cut">Saccharomyces cerevisiae mitochondrion</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
141 <option value="Eyeren.cut">Yersinia enterocolitica</option>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
142 </param>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
143 </section>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
144 </inputs>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
145 <outputs>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
146 <data name="constructs" format="xml" label="Constructs" />
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
147 </outputs>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
148 <tests>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
149 <test>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
150 <!-- test 1: check if identical outputs are produced with default parameters -->
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
151 <param name="genes_file" value="genes_lycopene.csv" />
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
152 <output name="constructs" >
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
153 <assert_contents>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
154 <is_valid_xml />
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
155 <has_text text='rdf:RDF xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#" xmlns:xsd1="http://www.w3.org/2001/XMLSchema#dateTime/" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" xmlns:synbiohub="http://synbiohub.org#" xmlns:sbh="http://wiki.synbiohub.org/wiki/Terms/synbiohub#" xmlns:sybio="http://www.sybio.ncl.ac.uk#" xmlns:ncbi="http://www.ncbi.nlm.nih.gov#" xmlns:igem="http://wiki.synbiohub.org/wiki/Terms/igem#" xmlns:genbank="http://www.ncbi.nlm.nih.gov/genbank#" xmlns:gbconv="http://sbols.org/genBankConversion#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:obo="http://purl.obolibrary.org/obo/"'/>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
156 </assert_contents>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
157 </output>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
158 </test>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
159 </tests>
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
160 <help><![CDATA[
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
161 OptDoE
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
162 ===========
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
163
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
164 An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The design is evaluated by its D-efficiency, defined as:
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
165
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
166 .. math:: D_{eff} = \frac{1}{n}\abs{X^{T}X}^{\frac{1}{p}}
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
167
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
168 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
169
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
170 Where n is the number of experimental runs or library size, p is the number of independent variables, and X is the model matrix, i.e., a row for each experimental run and a column for each term in the model. The library size n can be selected and should be above a minimal threshold depending on the number of combinatorial complexity of the library.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
171 The experimental design can be evaluated through the provided diagnostics for D-efficiency, power analysis, and relative prediction variance, allowing the optimal selection of library size.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
172 The resulting design is provided as an SBOL collection containing the definition of each DNA component and the combinatorial library of constructs.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
173
1
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
174 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/optdoe/img/image3.png
0
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
175 :width: 80 %
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
176 :align: center
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
177
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
178
1
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
179 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/optdoe/img/image46.png
0
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
180 :width: 80 %
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
181 :align: center
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
182
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
183 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
184
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
185 Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
186 Note: if advanced parameter "input_parts" is left empty, the following parts are used:
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
187
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
188
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
189 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
190 | Name | Type | SynBioHub |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
191 +=========+============+==================================================+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
192 | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
193 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
194 | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
195 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
196 | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
197 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
198 | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
199 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
200 | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
201 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
202 | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
203 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
204 | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 |
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
205 +---------+------------+--------------------------------------------------+
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
206
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
207 The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
208
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
209 Input
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
210 -----
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
211
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
212 Required:
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
213
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
214 * **Genes**\ : Output of Selenzyme. The CSV file contains four columnds: Name,Type,Part,Step. The column "Name" contains the Uniprot ID found by Selenzyme. The column "Type" represents the type of the "Part", a *gene*. The column "Part" has the same information as the column "Name". The column "Step" contains the order of the position in the pathway of the gene.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
215
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
216 Advanced options:
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
217
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
218 * **Optimised Genes**\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
219 * **Ref Parts**\ : CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
220 * **Maximal library size**\ : (integer, default: 32) Maximal number of constructs in the SBOL output.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
221 * **Get sequences**\ : (boolean, default: True) Grab the sequence for each part of the SBOL output.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
222 * **Back translate**\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
223 * **Codon Table**\ : (text, default: Eecoli.cut) Codon Usage Table. See `codon_table <https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBOSS+backtranseq+Help+and+Documentation#EMBOSSbacktranseqHelpandDocumentation-WebServices>`_ for more codons.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
224
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
225 Output
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
226 ------
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
227
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
228 * **Constructs**\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above.
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
229
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
230 Project Link
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
231 ------------
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
232
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
233 * `Original Project <https://github.com/pablocarb/doebase>`_
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
234
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
235 License
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
236 -------
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
237
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
238 `MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
239
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
240 Acknowledgments
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
241 ---------------
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
242
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
243 * Joan Hérisson
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
244 * Thomas Duigou
4f1acbf17618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
245 ]]></help>
1
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
246 <citations>
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
247 <citation type="bibtex">
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
248 @unpublished{pablocarb
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
249 author = {Pablo Carbonell},
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
250 title = {{doebase}},
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
251 url = {https://github.com/pablocarb/doebase/},
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
252 }
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
253 </citation>
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
254 </citations>
9a2fb8d83eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
parents: 0
diff changeset
255 </tool>