| Previous changeset 3:0eebff4180d9 (2017-11-02) Next changeset 5:e94b8b64929c (2018-08-24) |
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Commit message:
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac |
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modified:
tassel.xml |
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added:
test-data/Allele_effects.txt test-data/Best_K_Output test-data/Log_file.txt test-data/Tassel_output.txt test-data/input_hapmap.txt test-data/phenotyping_DRB.csv |
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| diff -r 0eebff4180d9 -r 652aafd88060 tassel.xml --- a/tassel.xml Thu Nov 02 05:19:30 2017 -0400 +++ b/tassel.xml Mon Apr 16 08:54:41 2018 -0400 |
| [ |
| @@ -1,8 +1,14 @@ -<tool id="Tassel" name="Tassel" version="5.0"> - <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description> +<tool id="Tassel" name="Tassel" version="2.0.0"> + <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> <requirements> - <requirement type="package" version="5.0">tassel</requirement> + <requirement type="package" version="5.2.40">tassel</requirement> </requirements> + + <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> + <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ #if $analysis_opts.fonction_selector == "mlm": -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq @@ -62,6 +68,8 @@ <when value="yes"> <param format="txt" name="structure" type="data" label="Structure file"/> </when> + <when value="no"> + </when> </conditional> </when> <when value="mlm"> @@ -75,6 +83,8 @@ <when value="yes"> <param format="txt" name="structure" type="data" label="Structure file"/> </when> + <when value="no"> + </when> </conditional> <param name="mlmVarCompEst" type="select" label="Variance Component Estimation"> <option value="P3D" selected="True">P3D</option> @@ -108,46 +118,64 @@ <data format="txt" name="log" label="Log file"/> </outputs> - <help> + + <tests> + <test> + <param name="hapmap" value="input_hapmap.txt"/> + <conditional name="analysis_opts"> + <param name="fonction_selector" value="glm"/> + <param name="trait" value="phenotyping_DRB.csv"/> + <conditional name="add_structure_file"> + <param name="additional_file_selector" value="yes"/> + <param name="structure" value="Best_K_Output"/> + </conditional> + </conditional> + <param name="filterAlignMinFreq" value="0.05"/> + <output name="output1" value="Tassel_output.txt"/> + <output name="output2" value="Allele_effects.txt"/> + </test> + </tests> + + <help><![CDATA[ + .. class:: infomark -**Program encapsulated in Galaxy by Southgreen** +**Tassel5** version 5.2.40 + +.. class:: infomark + +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Tassel** - ------ +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr -========== - Authors: -========== +--------------------------------------------------- -**Terry Casstevens** - ------ +======= +Tassel5 +======= -========== - Overview -========== +----------- +Description +----------- -Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. + | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. + | For further informations on tassel, please visit the website_. ------ +.. _website: http://www.maizegenetics.net/tassel/ -For further informations, please visite the website of TASSEL_. - - -.. _TASSEL: http://www.maizegenetics.net/tassel/ +------------ +Dependencies +------------ +Tassel5 + tassel_ 5.2.40, Conda version - </help> -<!-- -<tests> - <test> - <param name="input" value="genotyping_file.inp" /> - <output name="output" file="phase_output" /> - </test> -</tests> ---> +.. _tassel: https://anaconda.org/bioconda/tassel + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btm308</citation> + </citations> </tool> |
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| diff -r 0eebff4180d9 -r 652aafd88060 test-data/Allele_effects.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Allele_effects.txt Mon Apr 16 08:54:41 2018 -0400 |
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| b'@@ -0,0 +1,24727 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| diff -r 0eebff4180d9 -r 652aafd88060 test-data/Best_K_Output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Best_K_Output Mon Apr 16 08:54:41 2018 -0400 |
| b |
| b'@@ -0,0 +1,169 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\t9.99729E-05\t0.972056\t0.0276439\n+PADIBOENAR\t9.99819E-05\t9.99819E-05\t0.0428095\t0.87675\t0.0802405\n+PADIKASALLE\t0.0457639\t9.9982E-05\t9.9982E-05\t0.650692\t0.303344\n+POENOETHITAM\t9.9982E-05\t9.9982E-05\t0.0785051\t0.854046\t0.0672487\n+REKETMAUN\t9.9991E-05\t0.0163345\t0.0370753\t0.842761\t0.10373\n+AZUCENA\t0.092797\t9.9982E-05\t0.0419964\t9.9982E-05\t0.865007\n+MOROBEREKAN\t9.9991E-05\t0.0157051\t0.258976\t0.0396261\t0.685592\n+ARIAS\t0.00987816\t9.9991E-05\t0.20136\t0.00112785\t0.787534\n+BAGANANASALAO\t0.0843221\t9.9982E-05\t0.00120662\t9.9982E-05\t0.914271\n+BAKUNGH\t0.0697686\t0.00175448\t0.0652083\t9.9991E-05\t0.863169\n+BENGALYVAKARINA\t9.9982E-05\t9.9982E-05\t0.16583\t0.0601385\t0.773832\n+BINULAWAN\t0.0542316\t9.9982E-05\t0.0311301\t9.9982E-05\t0.914438\n+CAAWA_FORTUNA6\t0.0992445\t0.00435865\t0.0976843\t9.9991E-05\t0.798613\n+CANAROXA\t0.0713536\t9.9982E-05\t0.259436\t9.9982E-05\t0.66901\n+CUBA65\t0.122623\t9.9982E-05\t0.0871643\t9.9982E-05\t0.790013\n+DAVAO\t0.0641412\t9.9991E-05\t0.0961944\t0.00409284\t0.835472\n+DINORADO\t0.0401976\t9.9991E-05\t0.0538042\t0.0279409\t0.877957\n+FOHISOMOTRA\t9.9982E-05\t0.0282191\t0.400081\t9.9982E-05\t0.5715\n+GANIGI\t0.00429342\t0.0540375\t0.044346\t0.0954791\t0.801844\n+GOGO\t9.9991E-05\t0.109078\t0.0676765\t0.182622\t0.640524\n+GOGOLEMPUK\t9.9982E-05\t0.0280142\t9.9982E-05\t0.126055\t0.845731\n+GOGOLEMPAK\t9.9982E-05\t0.0309655\t9.9982E-05\t0.129186\t0.839649\n+JIMBRUKJOLOWORO\t9.9982E-05\t0.0158507\t9.9982E-05\t0.091846\t0.892103\n+KANIRANGA\t9.9982E-05\t9.9982E-05\t0.0380109\t0.133723\t0.828067\n+KEDAYAN\t0.057003\t0.0767605\t0.024114\t9.9991E-05\t0.842023\n+KENDINGA5H\t0.180552\t9.99729E-05\t9.99729E-05\t9.99729E-05\t0.819148\n+KETANKONIR\t9.9991E-05\t0.0779645\t0.0142508\t0.0592726\t0.848412\n+KETANMENAH\t0.0201128\t0.0883115\t0.0648225\t9.9991E-05\t0.826653\n+KINANDANGPATONG\t0.115686\t0.0295723\t0.229231\t9.9991E-05\t0.62541\n+KOMOJAMANITRA\t9.9982E-05\t9.9982E-05\t0.260656\t0.0653909\t0.673754\n+KUROKA\t9.9991E-05\t0.268526\t0.0192416\t0.127015\t0.585118\n+LUDAN\t0.0564957\t9.9991E-05\t0.0219148\t0.00218359\t0.919306\n+MAINTIMOLOTSY1226\t9.9982E-05\t9.9982E-05\t0.484856\t0.00805619\t0.506887\n+MALAGKITPIRURUTONG\t0.107599\t0.0167934\t0.121131\t0.0170213\t0.737455\n+PALAWAN\t0.191374\t9.9982E-05\t0.0190776\t9.9982E-05\t0.789349\n+PATEBLANCMAN1\t9.9991E-05\t0.0132222\t0.223095\t0.0285711\t0.735011\n+PULULAPA\t9.9991E-05\t0.0442492\t0.106133\t0.0803845\t0.769133\n+RATHAL\t9.9991E-05\t0.0441769\t0.153132\t0.0418184\t0.760773\n+SPEAKER\t0.103825\t9.9982E-05\t0.0321583\t9.9982E-05\t0.863816\n+TANDUI\t0.0195044\t0.0732579\t0.0090131\t9.9991E-05\t0.898125\n+TREMBESE\t9.9982E-05\t0.0456224\t9.9982E-05\t0.0874228\t0.866755\n+VARYMADINIKA3566\t9.9973E-05\t9.9973E-05\t0.245999\t9.9973E-05\t0.753701\n+VARYMALADY\t9.9991E-05\t0.0291979\t0.131621\t0.0919368\t0.747144\n+VARYSOMOTRASIHANAKA\t9.9982E-05\t0.0220298\t0.364861\t9.9982E-05\t0.61291\n+YANCAOUSSA\t9.9991E-05\t0.0123733\t0.255451\t0.0334045\t0.698671\n+IR47686-09-01-B-1\t0.0814244\t9.9991E-05\t0.295263\t0.000550324\t0.622662\n+IR53236-275-1\t0.0752619\t9.9982E-05\t0.341504\t9.9982E-05\t0.583034\n+CUIABANA\t9.9991E-05\t0.440717\t0.396495\t0.0261122\t0.136576\n+IRAT212\t9.9991E-05\t0.118062\t0.394228\t0.0439711\t0.443639\n+JUMALI\t0.119868\t0.386982\t9.99821E-05\t0.49295\t9.99821E-05\n+MANANELATRA520\t9.9982E-05\t9.9982E-05\t0.490005\t0.0316006\t0.478194\n+P5589-1-1-3-P\t0.46478\t9.9991E-05\t0.417267\t0.0328256\t0.0850272\n+PACHOLINHA\t0.0479934\t9.9982E-05\t0.489494\t9.9982E-05\t0.462313\n+IR66421-105-1-1\t0.432283\t0.0614641\t0.28006\t0.0501976\t0.175996\n+IR71524-44-1-1\t0.371651\t9.9991E-05\t0.462814\t0.0102341\t0.155201\n+PRIMAVERA\t0.0547671\t0.0936009\t0.419272\t0.0642728\t0.368088\n' |
| b |
| diff -r 0eebff4180d9 -r 652aafd88060 test-data/Log_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Log_file.txt Mon Apr 16 08:54:41 2018 -0400 |
| [ |
| b'@@ -0,0 +1,59 @@\n+/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/LiuExt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/sqlite-jdbc-3.8.4.3-SNAPSHOT.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/itextpdf-5.1.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-alignment-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-css.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xmlParserAPIs.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/poi-3.0.1-FINAL-20070705.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-awt-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/jcommon-1.0.6.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/snappy-java-1.1.1.6.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/commons-codec-1.10.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/log4j-1.2.13.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-phylo-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xml.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/geronimo-spec-activation-1.0.2-rc4.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/json-simple-1.1.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/jfreechart-1.0.3.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-xml.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/colt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-dom.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-core-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/junit-4.10.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-gui-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-ext.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/trove-3.0.3.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/mail-1.4.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/ejml-0.23.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-gvt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/forester.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/commons-math3-3.4.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/guava-14.0.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xercesImpl.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-svg-dom.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0'..b'FO net.maizegenetics.analysis.filter.FilterAlignmentPlugin - Resulting Number Sites: 12363\n+[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.filter.FilterAlignmentPlugin: progress: 100%\n+[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%\n+[main] WARN net.maizegenetics.pipeline.TasselPipeline - parseArgs: NOTE: The -glm flags are deprecated.\n+parseArgs: PLEASE RUN THIS COMMAND TO GET USAGE: ./run_pipeline.pl -FixedEffectLMPlugin\n+\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: progress: 100%\n+[Thread-35] INFO net.maizegenetics.plugindef.AbstractPlugin - \n+FixedEffectLMPlugin Parameters\n+phenoOnly: false\n+saveToFile: false\n+siteFile: null\n+alleleFile: null\n+maxP: 1.0\n+permute: false\n+nperm: 0\n+genotypeComponent: Genotype\n+\n+[Thread-35] INFO net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory - TasselBlas library for system-specific BLAS/LAPACK not found. Using system-independent EJML for DoubleMatrix operations.\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 0%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 10%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 20%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 30%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 40%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 50%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 60%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 70%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 80%\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 90%\n+[Thread-35] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: GLM_Stats_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 to file: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM1.txt\n+[Thread-35] INFO net.maizegenetics.analysis.data.ExportMultiplePlugin - Datum: GLM_Stats_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 Written to: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM1.txt\n+[Thread-35] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: GLM_Genotypes_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 to file: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM2.txt\n+[Thread-35] INFO net.maizegenetics.analysis.data.ExportMultiplePlugin - Datum: GLM_Genotypes_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 Written to: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM2.txt\n+[Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 100%\n' |
| b |
| diff -r 0eebff4180d9 -r 652aafd88060 test-data/Tassel_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Tassel_output.txt Mon Apr 16 08:54:41 2018 -0400 |
| b |
| b'@@ -0,0 +1,12364 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|
| b |
| diff -r 0eebff4180d9 -r 652aafd88060 test-data/input_hapmap.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_hapmap.txt Mon Apr 16 08:54:41 2018 -0400 |
| b |
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\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tG\tG\tA\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\n+Chr12:27388608\tG/A\t12\t27388608\t+\tNA\tNA\tNA\tNA\tNA\tNA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tA\tA\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\tG\n' |
| b |
| diff -r 0eebff4180d9 -r 652aafd88060 test-data/phenotyping_DRB.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotyping_DRB.csv Mon Apr 16 08:54:41 2018 -0400 |
| b |
| @@ -0,0 +1,168 @@ +<Trait> Deeprootbiomass +62667 0.0313 +63-104 0.0225 +ARAGUAIA 0.0457 +ARIAS 0.0152 +ARROZCEBADA 0.0075 +AZUCENA 0.0471 +BABER 0.0094 +BAGANANASALAO 0.0116 +BAKUNGH 0.0129 +BENGALYVAKARINA 0.0121 +BICOBRANCO 0.0218 +BINULAWAN 0.0044 +BULUPANDAK 0.0123 +CAAWA/FORTUNA6 0.0349 +CAIAPO 0.025 +CANAROXA 0.0181 +CANELADEFERRO 0.0418 +CHALOYOE 0.0355 +CHAPHUMA 0.0492 +CHUAN3 0.0639 +CHUAN4 0.0684 +CICIHBETON 0.0222 +CIRAD358 0.0154 +CIRAD392 0.0285 +CIRAD394 0.0384 +CIRAD403 0.0118 +CIRAD409 0.0082 +CIRAD488 0.0222 +CNA-7\BO\1\1>33-13-6-1 0.015 +COLOMBIA1 0.0014 +CT13582-15-5-M 0.0209 +CUBA65 0.0226 +CUIABANA 0.0158 +CURINCA 0.0122 +DAM 0.0089 +DANGREY 0.0164 +DAVAO 0.0395 +DAWASANRED 0.0155 +DINORADO 0.0161 +DOURADOAGULHA 0.0674 +DOURADOPRECOCE 0.0459 +EARLYMUTANTIAC165 0.0257 +ESPERANZA 0.0216 +FOHISOMOTRA 0.0257 +GANIGI 0.0451 +GEMJYAJYANAM 0.0138 +GIZA171 0.014 +GOGO 0.0053 +GOGOLEMPAK 0.0738 +GOGOLEMPUK 0.062 +GOMPA2 0.0376 +GRAZI 0.0285 +GUARANI 0.0203 +GUNDILKUNING 0.0307 +HAWMOM 0.0196 +HD1-4 0.0211 +IAC165 0.0442 +IAC25 0.0328 +IAC47 0.0239 +IDSA77 0.0216 +IGUAPECATETO 0.0287 +INDANE 0.0202 +IR47684-05-1-B 0.0134 +IR47686-09-01-B-1 0.0148 +IR53236-275-1 0.0449 +IR60080-46A 0.0218 +IR63372-08 0.0159 +IR63380-16 0.0127 +IR65261-19-1-B 0.0264 +IR65907-188-1-B 0.0261 +IR65907-206-4-B 0.0203 +IR66421-096-2-1-1 0.0047 +IR66421-105-1-1 0.0033 +IR68704-145-1-1-B 0.0127 +IR71524-44-1-1 0.0456 +IR71525-19-1-1 0.0263 +IRAT104 0.04 +IRAT109 0.0153 +IRAT112 0.024 +IRAT13 0.0522 +IRAT144 0.0396 +IRAT170 0.0293 +IRAT177 0.0349 +IRAT2 0.0231 +IRAT212 0.0087 +IRAT216 0.0049 +IRAT234 0.0126 +IRAT257 0.0255 +IRAT335 0.0114 +IRAT362 0.0369 +IRAT364 0.0289 +IRAT366 0.0114 +IRAT380 0.0155 +JAOHAW 0.0725 +JIMBRUKJOLOWORO 0.041 +JUMALI 0.0283 +JUMULA2 0.0046 +KAKANI2 0.0162 +KANIRANGA 0.0333 +KARASUKARASURANKASU 0.0678 +KEDAYAN 0.0093 +KENDINGA5H 0.06 +KETANKONIR 0.055 +KETANLUMBU 0.0205 +KETANMENAH 0.042 +KHAODAM 0.0622 +KHAOKAPXANG 0.0418 +KINANDANGPATONG 0.0295 +KOMOJAMANITRA 0.0171 +KU115 0.0355 +KUROKA 0.0139 +LAMBAYQUE1 0.0222 +LUDAN 0.017 +M202 0.0152 +MAHAE 0.0439 +MAINTIMOLOTSY1226 0.0109 +MALAGKITPIRURUTONG 0.0187 +MANANELATRA520 0.0074 +MANDRIRAVINA3512 0.0244 +MARAVILHA 0.0065 +MITSANGANAHIJERY 0.0347 +MOLOK 0.0192 +MOROBEREKAN 0.0328 +NABESHI 0.035 +NEPHOAVANG 0.0114 +NHTA10 0.0516 +NHTA5 0.0493 +NIPPONBARE 0.0093 +NPE253 0.0062 +NPE826 0.0116 +ORYZICASABANA6 0.0438 +OS4 0.0121 +OS6 0.0251 +P5589-1-1-3-P 0.0126 +PACHOLINHA 0.0179 +PADIBOENAR 0.0158 +PADIKASALLE 0.0068 +PALAWAN 0.0293 +PATEBLANCMAN1 0.0315 +PCT11\0\0\2.BO\1>55-1-3-1 0.0089 +PCT4\SA\4\1>1076-2-4-1-5 0.0076 +PEHPINUO 0.0462 +POENOETHITAM 0.0114 +PRIMAVERA 0.0096 +PULULAPA 0.0183 +RATHAL 0.008 +REKETMAUN 0.0106 +RT1031-69 0.0221 +SENG 0.0168 +SPEAKER 0.0177 +TANDUI 0.0007 +TREMBESE 0.0425 +TRESMESES 0.0463 +TSIPALA89 0.0284 +VARYLAVA90 0.0527 +VARYLAVADEBETAFO 0.0105 +VARYMADINIKA3566 0.0112 +VARYMALADY 0.0221 +VARYSOMOTRASIHANAKA 0.0113 +VIETNAM1 0.041 +VIETNAM3 0.0298 +WAB56-125 0.0261 +WAB56-50 0.0225 +WAB706-3-4-K4-KB-1 0.041 +YANCAOUSSA 0.0341 +YANGKUMRED 0.0294 +YUNLU7 0.0728 |