# HG changeset patch # User tduigou # Date 1648477019 0 # Node ID 8a087d7546b85aeb5f4e2073a60d9b91e3c219c4 # Parent de9f53630349c6a6d1313b9aac955838ed507735 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty" diff -r de9f53630349 -r 8a087d7546b8 rpbasicdesign.xml --- a/rpbasicdesign.xml Wed Dec 15 15:10:43 2021 +0000 +++ b/rpbasicdesign.xml Mon Mar 28 14:16:59 2022 +0000 @@ -1,7 +1,10 @@ - + Build DNA-BOT input files from rpSBML + + 1.0.1 + - rpbasicdesign + rpbasicdesign - - - + + + + + + + + + + + + [0-9a-zA-Z_:-]+ + +

- - - - + + + + + + + + + + + + + + + + + + + + + + + + + +

- - - - + + + + + adv['sbol_output'] - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - @article{10.1093/synbio/ysaa010, - author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, - title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, - journal = {Synthetic Biology}, - volume = {5}, - number = {1}, - year = {2020}, - month = {07}, - issn = {2397-7000}, - doi = {10.1093/synbio/ysaa010}, - url = {https://doi.org/10.1093/synbio/ysaa010}, - note = {ysaa010}, - eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, - } - + 10.1093/synbio/ysaa010 \ No newline at end of file diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_A1.xml --- a/test-data/BASIC_construct_A1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - - - - 1 - - - - LMS - - - - - - - 1 - BASIC_SEVA_37_CmR_p15A_1 - - - - LMP - - 1 - - - - - 1 - - - PJ23119_BASIC - - - - - - - U1_RBS1 - - 1 - - - - - - 1 - - - P21684 - - - U2_RBS1 - - 1 - - - - - - P21683 - 1 - - - - - - - - 1 - - U3_RBS2 - - - - - - - P21685 - - - 1 - - - - - U3_RBS2_0 - - - 1 - - - - - - 1 - - constraint_5 - - - - - - - - - constraint_7 - - 1 - - - - - 1 - - - 1 - - - - U1_RBS1_0 - - - - - - - BASIC_SEVA_37_CmR_p15A_1_0 - 1 - - - - - - 1 - - P21684_0 - - - - - - - - - LMS_0 - 1 - - - - - - - 1 - LMP_0 - - - - - - - 1 - - - P21683_0 - - - - - - - - - - - - 1 - constraint_8 - - - - - constraint_2 - - - 1 - - - - - - BASIC_construct_A1 - - - constraint_0 - 1 - - - - - - - - - - - constraint_6 - - 1 - - - - - - - 1 - PJ23119_BASIC_0 - - - - - - - - - 1 - U2_RBS1_0 - - - - - - - 1 - - - constraint_3 - - - - - - - 1 - - P21685_0 - - - - - - - - - - constraint_1 - 1 - - - - - - - - 1 - - constraint_4 - - - - - - 1 - - LMS - - - - BASIC_SEVA_37_CmR_p15A_1 - - - - 1 - - - - 1 - LMP - - - - - - 1 - - - PJ23119_BASIC - - - - - U1_RBS1 - 1 - - - - - atgc - 1 - - P21684 - - - U2_RBS1 - - - - 1 - - - - - P21683 - atgc - 1 - - - - 1 - - U3_RBS2 - - - - - atgc - 1 - P21685 - - - diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_B1.xml --- a/test-data/BASIC_construct_B1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - - - - 1 - - - - LMS - - - - - - - 1 - BASIC_SEVA_37_CmR_p15A_1 - - - - LMP - - 1 - - - - - - PJ23101_BASIC - - - - 1 - - - U1_RBS3 - - 1 - - - - - - - - 1 - - - P21684 - - - U2_RBS1 - - 1 - - - - - - P21683 - 1 - - - - - - - - 1 - - U3_RBS2 - - - - - - - P21685 - - - 1 - - - - - - 1 - - - constraint_1 - - - - - - - P21684_0 - 1 - - - - - - - - - 1 - constraint_7 - - - - - - - - - - 1 - - U2_RBS1_0 - - - - - BASIC_SEVA_37_CmR_p15A_1_0 - - 1 - - - - - - - constraint_3 - - - 1 - - - - - - - - - constraint_6 - - 1 - - - - - - - U3_RBS2_0 - 1 - - - - - - - - - constraint_4 - - 1 - - - - - - - 1 - - - - U1_RBS3_0 - - - - - - constraint_5 - 1 - - - - - - - - - 1 - LMP_0 - - - - - - - - - 1 - - LMS_0 - - - - BASIC_construct_B1 - - - P21685_0 - - - - 1 - - - - - 1 - - - PJ23101_BASIC_0 - - - - - - - - - 1 - constraint_8 - - - - - - - P21683_0 - - - 1 - - - - - - 1 - - constraint_0 - - - - - 1 - - - 1 - - - - constraint_2 - - - - - - - 1 - - LMS - - - - BASIC_SEVA_37_CmR_p15A_1 - - - - 1 - - - - 1 - LMP - - - - - - PJ23101_BASIC - - - 1 - - - - - - 1 - U1_RBS3 - - - - atgc - 1 - - P21684 - - - U2_RBS1 - - - - 1 - - - - - P21683 - atgc - 1 - - - - 1 - - U3_RBS2 - - - - - atgc - 1 - P21685 - - - diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_C1.xml --- a/test-data/BASIC_construct_C1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - - - - 1 - - - - LMS - - - - - - - 1 - BASIC_SEVA_37_CmR_p15A_1 - - - - LMP - - 1 - - - - - - PJ23101_BASIC - - - - 1 - - - - - U1_RBS1 - - 1 - - - - - - 1 - - - P21684 - - - - 1 - - U3_RBS2 - - - - - - - P21685 - - - 1 - - - - - U2_RBS2 - - - 1 - - - P21683 - 1 - - - - - - - - - - - 1 - - - P21685_0 - - - - - BASIC_SEVA_37_CmR_p15A_1_0 - - 1 - - - - - - - - 1 - - - P21684_0 - - - 1 - - - - - - constraint_6 - 1 - - - - - - constraint_4 - - - - 1 - - - - - - - 1 - LMP_0 - - - - - - - - P21683_0 - - 1 - - - - - - - - U2_RBS2_0 - 1 - - - - - - - - - - - 1 - constraint_5 - - - - - - constraint_8 - - 1 - - - - - - - constraint_2 - - - - - 1 - - - - - 1 - - - - constraint_3 - - - - - - LMS_0 - 1 - - - - - - - - - U1_RBS1_0 - 1 - - - - - - - - - - 1 - - constraint_1 - - - - - - U3_RBS2_0 - 1 - - - - - - - - - - constraint_7 - - - 1 - - - BASIC_construct_C1 - - - - - constraint_0 - - 1 - - - - - - - - - PJ23101_BASIC_0 - 1 - - - - - - 1 - - LMS - - - - BASIC_SEVA_37_CmR_p15A_1 - - - - 1 - - - - 1 - LMP - - - - - - PJ23101_BASIC - - - 1 - - - - - U1_RBS1 - 1 - - - - - atgc - 1 - - P21684 - - - - 1 - - U3_RBS2 - - - - - atgc - 1 - P21685 - - - - U2_RBS2 - - 1 - - - - - - - P21683 - atgc - 1 - - diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate.csv --- a/test-data/biolegio_plate.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -L1-S,A1, -L1-P,B1, -L2-S,A2, -L2-P,B2, -L3-S,A3, -L3-P,B3, -L4-S,A4, -L4-P,B4, -L5-S,A5, -L5-P,B5, -L6-S,A6, -L6-P,B6, -LMP-S,A7, -LMP-P,B7, -LMS-S,A8, -LMS-P,B8, -U1-S,C1, -U2-S,C2, -U3-S,C3, -U1-RBS1-P,C4, -U1-RBS2-P,C5, -U1-RBS3-P,C6, -U1-A01-P,D1, -U1-A02-P,D2, -U1-A03-P,D3, -U1-A04-P,D4, -U1-A05-P,D5, -U1-A06-P,D6, -U1-A07-P,D7, -U1-A08-P,D8, -U1-A09-P,D9, -U1-A10-P,D10, -U1-A11-P,D11 -U1-A12-P,D12, -U2-RBS1-P,C7, -U2-RBS2-P,C8, -U2-RBS3-P,C9, -U2-A01-P,E1, -U2-A02-P,E2, -U2-A03-P,E3, -U2-A04-P,E4, -U2-A05-P,E5, -U2-A06-P,E6, -U2-A07-P,E7, -U2-A08-P,E8, -U2-A09-P,E9, -U2-A10-P,E10, -U2-A11-P,E11 -U2-A12-P,E12, -U3-RBS1-P,C10, -U3-RBS2-P,C11, -U3-RBS3-P,C12, -U3-A01-P,F1, -U3-A02-P,F2, -U3-A03-P,F3, -U3-A04-P,F4, -U3-A05-P,F5, -U3-A06-P,F6, -U3-A07-P,F7, -U3-A08-P,F8, -U3-A09-P,F9, -U3-A10-P,F10, -U3-A11-P,F11 -U3-A12-P,F12, -U1-AM12-P,A10, -U1-AM24-P,B10, -U2-AM12-P,A11, -U2-AM24-P,B11, -U3-AM12-P,A12, -U3-AM24-P,B12, -LF1-S,A9, -LF1-P,B9, -LF2-S,G1, -LF2-P,H1, -LF3-S,G2, -LF3-P,H2, -LF4-S,G3, -LF4-P,H3, -LF5-S,G4, -LF5-P,H4, -LF6-S,G5, -LF6-P,H5, \ No newline at end of file diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate_lycopene.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate_muconate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_muconate.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs.csv --- a/test-data/constructs.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 -A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,, diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs_lycopene.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,, diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs_muconate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_muconate.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,89 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,, 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