| Next changeset 1:6362669c440a (2015-10-02) |
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Commit message:
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added:
fastMe_main/fastme.xml fastMe_main/test-data/newick fastMe_main/test-data/newick.log fastMe_main/test-data/phylip fastMe_main/tool_dependencies.xml |
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| diff -r 000000000000 -r 3ef62be50f9d fastMe_main/fastme.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastMe_main/fastme.xml Wed Jul 01 10:43:05 2015 -0400 |
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| @@ -0,0 +1,237 @@ +<tool id="sniplay_fastme" name="FastME" version="1.0.2"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Calculate distance tree for an alignment file</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package" version="2.1.4">fastme</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command> + fastme --input_data=$input_data --dna=$model --output_tree=$fileout + #if str( $distance ) == "SPR": + --spr + #elif str( $distance )[:3] == "NNI" : + #if str( $distance ) == "NNI_B" : + --nni=B + #else : + --nni=O + #end if + + #else : + --method=$distance + #end if + > $fileout_log + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" /> + <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" /> + <param name="model" type="select" label="Evolutionary model" > + <option value="p">p-distance</option> + <option value="Y">RY symetric</option> + <option value="R">RY</option> + <option value="J">JC69</option> + <option value="K">K2P</option> + <option value="1">F81</option> + <option value="4" selected="true">F84</option> + <option value="T">TN93</option> + <option value="L">LogDet</option> + </param> + <param name="distance" type="select" label="Distance methode" > + <option value="B">TaxAdd_BalME</option> + <option value="O">TaxAdd_OLSME</option> + <option value="I" selected="true">BIONJ</option> + <option value="N">NJ</option> + <option value="U">UNJ</option> + <option value="NNI_B">NNI_BalME</option> + <option value="NNI_O">NNI_OLS</option> + <option value="SPR">SPR</option> + </param> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> + <data name="fileout" type="data" format="txt" label="${fileout_label}" /> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + + <test> + <param name="filein" value="phylip" /> + <param name="model" value="4"/> + <param name="distance" value="I"/> + <output name="fileout" file="newick" /> + <output name="fileout_log" file="newick.log" /> + </test> + + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + +.. class:: infomark + +**Authors** + + | Richard Desper and Olivier Gascuel, + | Journal of Computational Biology 19(5), 687-705, 2002. + | Molecular Biology and Evolution 21(3), 587-598, 2004. + | Please cite these papers if you use this software in your publications. + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + + +====== +FastMe +====== + +----------- +Description +----------- + + FastME - A distance based phylogeny reconstruction algorithm. + + FastME showed better topological accuracy than NJ, + BIONJ, WEIGHBOR and FITCH, in all evolutionary + conditions we tested, which include large range + deviations from molecular clock and substitution rates. + + + +----------------- +Workflow position +----------------- + +**Upstream tools** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +Readseq phylip conversion phylip +=========== ========================== ======= + + +**Downstream tools** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +Rooting out tree Newick +=========== ========================== ======= + + +---------- +Input file +---------- + +Phylip file + Phylip file with sequence alignments + + +---------- +Parameters +---------- + +Output name + Output base name for the ouput files + +Evolutionary model + Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet. + +Distance methode + FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR + +------------ +Output files +------------ + +Output_name + Resulting tree at Newick format + +Output_name.log + Log file + +------------ +Dependencies +------------ +FastME + http://www.atgc-montpellier.fr/fastme + + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Philip file +----------- + +:: + + 168 5125 + IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT + KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT + +Parameters +========== + +Output name -> Newick tree + +Evolutionary model -> F84 + +Distance methode -> BIONJ + +Output files +============ + +Newick tree +----------- + +:: + + (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... + + + </help> + +</tool> |
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| diff -r 000000000000 -r 3ef62be50f9d fastMe_main/test-data/newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastMe_main/test-data/newick Wed Jul 01 10:43:05 2015 -0400 |
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| @@ -0,0 +1,2 @@ +(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); + |
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| diff -r 000000000000 -r 3ef62be50f9d fastMe_main/test-data/newick.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastMe_main/test-data/newick.log Wed Jul 01 10:43:05 2015 -0400 |
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| @@ -0,0 +1,10 @@ + + . This analysis will run on 2 threads. + +# Analysing dataset 1 + + . Computing pairwise distances... + + . Computing tree... + + . Time used 0h00m05s |
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| diff -r 000000000000 -r 3ef62be50f9d fastMe_main/test-data/phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastMe_main/test-data/phylip Wed Jul 01 10:43:05 2015 -0400 |
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| b'@@ -0,0 +1,17579 @@\n+ 168 5125\n+IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT\n+DOURADOPRE AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KINANDANGP GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+CAAWA/FORT GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+VARYLAVA90 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+CIRAD358 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAAATCAAAT\n+PCT4_SA_4_ GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+YUNLU7 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BAKUNGH GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BAGANANASA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+NHTA10 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATAATAAAG TAATACTAAT\n+MALAGKITPI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+IR65907-20 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KAKANI2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATAAAAAGAT\n+DOURADOAGU AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IRAT13 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+DAWASANRED GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTACTAAAG TAATACTAAT\n+CHUAN4 GCGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTACGAAAG TAATACTAAT\n+MOROBEREKA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IRAT362 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+PULULAPA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+MAHAE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA GGAACGAAAG TAATACTAAT\n+WAB56-50 AAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+ORYZICASAB AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+MARAVILHA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IDSA77 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+INDANE GAGAACCGTC CTGTAAGTAC TCTTGTTATA AGAACTAAAG TAATACTAAT\n+DINORADO GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+RT1031-69 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IR63380-16 GAAATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+VARYSOMOTR GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+HAWMOM GAGAACCGTC CTGTAAGTAC TCTTGCTTAA AATACGAAAG TAATACTAAT\n+IRAT364 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+TREMBESE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATTAAG TAATACTAAT\n+NIPPONBARE GAAAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TATTACTAAT\n+AZUCENA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+BABER GAGAACCGTC CTGTAACCTT GATTGTTATA AGAAATAAAG TAATACTAAT\n+WAB56-125 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BENGALYVAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAAAT\n+KETANMENAH GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n+BULUPANDAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+ARIAS GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n+GOMPA2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATTAAAAAAT\n+IRAT335 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+M202 GAGAACCGTC CTGTAACCTT GATTGTTATA GGTAATAAAG TAATACTAAT\n+IR53236-27 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IR65907-18 GAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+P5589-1-1- AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+MANDRIRAVI AAGAACCGTC CTGTAAGTAC TCTTGCTTAA AGTAATAAAG TAATACTAAT\n+PALAWAN GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAACTAAAG TATATCAACA\n+CNA-7_BO_1 GAGTACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAAAAAAGAT\n+IRAT257 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+TANDUI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+KETANLUMBU GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+IRAT109 GAGAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TAATACTAAT\n+PCT11_0_0_ AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KANIRANGA GAGAACCGTC CTGTAAGTAC'..b'\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCAGTACT GACTGCCTGA ATGTT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ AAACGGTACT ATCTGCTAAA TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n' |
| b |
| diff -r 000000000000 -r 3ef62be50f9d fastMe_main/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastMe_main/tool_dependencies.xml Wed Jul 01 10:43:05 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastme" version="2.1.4"> + <repository changeset_revision="fbf2a5cac7e3" name="package_fastme_2_1_4" owner="gandres" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |