Mercurial > repos > rplanel > ccqtl_permutations
changeset 0:6b6c9ab21674 draft
planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/ccqtl commit 320b3741bd00d1707829822302abe0f0b610981a
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ccqtl-permutations.xml Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,52 @@ +<tool id="ccqtl_permutations" name="CCQTL: Run permutations" version="@TOOL_VERSION@+@WRAPPER_VERSION@" python_template_version="3.5"> + <description>to define significance thresholds</description> + <macros> + <token name="@WRAPPER_VERSION@">galaxy0</token> + <import>macros.xml</import> + </macros> + <edam_topics> + <edam_topic>topic_0625</edam_topic> + <edam_topic>topic_0160</edam_topic> + <edam_topic>topic_3338</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3232</edam_operation> + </edam_operations> + <requirements> + <expand macro="requirements"/> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + @BASE_CMD@ + permutations + --n_perm ${n_perm} + --crossdata ${crossdata} + --clean_pr ${clean_pr} + --kloco ${kloco} + --covar_modmat ${covar_modmat} + #if $strat_covar != '': + --strat_covar ${strat_covar} + #end if + ]]> + </command> + <inputs> + <expand macro="crossdata"/> + <expand macro="clean_pr"/> + <expand macro="kloco"/> + <param argument="--n_perm" type="integer" value="2" min="0" max="1000" label="Number of permutations (recommended minimum: 100)"/> + <param argument="--covar_modmat" type="data" format="rds" label="covar_modmat object (rds)"/> + <param argument="--strat_covar" type="text" value="" label="List of covariates used to stratify permutations on." help="At most three covariates, all must be categorical and previously passed as covariate at the genome_scan step. Typical stratification covariate is sex."/> + </inputs> + <outputs> + <data format="rds" name="operm_lmm" from_work_dir="outfiles/Rdata/operm_lmm.rds" label="${tool.name} on ${on_string}: operm_lmm.rds"/> + <data format="rds" name="covar_permstrata" from_work_dir="outfiles/Rdata/covar_permstrata.rds" label="${tool.name} on ${on_string}: covar_permstrata.rds"/> + <data format="rds" name="stratcovar_modmat" from_work_dir="outfiles/Rdata/stratcovar_modmat.rds" label="${tool.name} on ${on_string}: stratcovar_modmat.rds"/> + <data format="rds" name="nrep_rds" from_work_dir="outfiles/Rdata/nrep.rds" label="${tool.name} on ${on_string}: nrep.rds"/> + </outputs> + <help> + <![CDATA[ + Compute permutations + ]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,48 @@ +<macros> + <token name="@TOOL_VERSION@">0.0.1_beta.2</token> + <xml name="requirements"> + <requirement type="package" version="@TOOL_VERSION@">r-ccqtl</requirement> + <yield/> + </xml> + <token name="@BASE_CMD@"> + ccqtl --cores \${GALAXY_SLOTS:-1} + </token> + <xml name="indiv_marker"> + <param name="indiv_marker" argument="--indiv_geno" type="select" label="Select individual genotypes of each CC mouse at each marker" help="Directory that contains the individual genotypes of each CC mouse at each marker and the funnel codes if applicable."> + <options from_data_table="ccqtl"> + <filter type="static_value" column="1" value="indiv_marker"/> + <validator type="no_options" message="No dataset available for the selected input dataset"/> + </options> + </param> + </xml> + <xml name="marker_set"> + <param argument="--marker_set" type="select" label="Select the genetic and physical maps as well as the founder genotypes information" help="Directory that contains the genetic and physical maps as well as the founder genotypes information, for the different combinations of marker set and genome build."> + <options from_data_table="ccqtl"> + <filter type="static_value" column="1" value="marker_set"/> + <validator type="no_options" message="No dataset available for the selected input dataset"/> + </options> + </param> + </xml> + <xml name="crossdata"> + <param argument="--crossdata" type="data" format="rds" label="crossdata rds file" help="The cross rds file output from make_inputs"/> + </xml> + <xml name="kloco"> + <param argument="--kloco" type="data" format="rds" label="kloco rds file" help="the LOCO kinship rds file output from make_inputs"/> + </xml> + <xml name="clean_pr"> + <param argument="--clean_pr" type="data" format="rds" label="clean_pr ds file" help="The cleaned genotype probabilities rds file output from make_inputs"/> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{githubseqtk, + author = {Victoire Baillet, Rémi Planel, Vincent Guillemot, Pascal Campagne}, + year = {2023}, + title = {ccqtl}, + publisher = {Gitlab}, + journal = {Gitlab repository}, + url = {https://gitlab.pasteur.fr/cc-qtl/ccqtl}, +}</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccqtl.loc Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,10 @@ +# <unique_build_id> <dbkey> <display_name> <build> <doi> <description> <optional_description> <file_base_path> + +#CC_MMnGM indiv_marker CC_MMnGM m38 individual genotypes of each CC mouse at each marker and the funnel codes if applicable. (mega muga and giga muga) ${__HERE__}/ccqtl/indiv_marker/CC_MMnGM_ref +CC_MMnGM_test indiv_marker CC_MMnGM_test m38 individual genotypes of each CC mouse at each marker and the funnel codes if applicable. (mega muga and giga muga test) ${__HERE__}/ccqtl/indiv_marker/CC_MMnGM_test + +#MMnGM_m38 marker_set MMnGM_m38 m38 https://doi.org/10.6084/m9.figshare.5404762.v2 Marker set for mega muga and giga muga ${__HERE__}/ccqtl/marker_set/MMnGM_m38 +MMnGM_m38_test marker_set MMnGM_m38_test m38 https://doi.org/10.6084/m9.figshare.5404762.v2 Marker set for mega muga and giga muga test ${__HERE__}/ccqtl/marker_set/MMnGM_m38_test +#MM_m38 marker_set MM_m38 m38 https://doi.org/10.6084/m9.figshare.5404750.v2 Marker set for mega muga ${__HERE__}/ccqtl/marker_set/MM_m38 +#GM_m38 marker_set GM_m38 m38 https://doi.org/10.6084/m9.figshare.5404759.v2 Marker set for giga muga$ {__HERE__}/ccqtl/marker_set/GM_m38 +#cc_annotations_m38 cc_annotations Annotations m38 m38 https://doi.org/10.6084/m9.figshare.5280229.v3,10.6084/m9.figshare.5286019.v8 DNA seq variants segregating among the founders + gene annotation, subsetted to MGI annot ${__HERE__}/ccqtl/annotations/m38 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccqtl/indiv_marker/CC_MMnGM_test/cc_crossinfo.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,73 @@ +# Cross information for Collaborative Cross (CC) lines inferred from genotypes from Srivastava et al. (2017) doi:10.1534/genetics.116.198838, data at doi:10.5281/zenodo.377036 +# nrow 69 +# ncol 9 +id,A,B,C,D,E,F,G,H +CC001/Unc,2,5,3,1,4,8,6,7 +CC002/Unc,7,3,4,8,5,1,2,6 +CC003/Unc,5,1,7,2,8,3,6,4 +CC004/TauUnc,3,1,8,7,2,6,5,4 +CC005/TauUnc,4,1,2,3,6,7,8,5 +CC006/TauUnc,7,8,6,1,4,3,2,5 +CC007/Unc,2,1,5,3,8,7,6,4 +CC008/GeniUnc,8,5,2,1,3,7,4,6 +CC009/Unc,5,2,1,7,4,6,8,3 +CC010/GeniUnc,1,5,2,7,6,4,8,3 +CC011/Unc,5,4,2,6,1,7,8,3 +CC012/GeniUnc,2,7,3,6,5,4,8,1 +CC013/GeniUnc,5,4,3,6,8,1,7,2 +CC015/Unc,1,5,6,7,4,2,8,3 +CC016/GeniUnc,8,2,6,5,4,3,7,1 +CC017/Unc,3,7,8,1,6,4,5,2 +CC018/Unc,2,3,6,1,8,7,5,4 +CC019/TauUnc,5,1,2,6,4,8,7,3 +CC020/GeniUnc,7,6,8,4,5,1,3,2 +CC021/Unc,7,3,6,8,4,5,1,2 +CC022/GeniUnc,1,8,4,5,6,2,3,7 +CC023/GeniUnc,4,2,8,5,7,6,3,1 +CC024/GeniUnc,1,2,6,8,5,3,7,4 +CC025/GeniUnc,6,5,3,2,7,8,1,4 +CC026/GeniUnc,6,3,4,7,1,8,2,5 +CC027/GeniUnc,6,4,3,5,1,7,8,2 +CC028/GeniUnc,5,2,4,7,1,3,8,6 +CC029/Unc,8,3,4,1,6,7,2,5 +CC030/GeniUnc,6,5,1,7,2,8,4,3 +CC031/GeniUnc,1,6,5,3,7,2,4,8 +CC032/GeniUnc,1,4,2,3,6,5,8,7 +CC033/GeniUnc,6,5,3,7,1,2,4,8 +CC034/Unc,8,3,7,1,2,5,6,4 +CC035/Unc,6,5,7,8,3,2,4,1 +CC036/Unc,2,6,3,5,8,1,7,4 +CC037/TauUnc,3,4,8,7,6,1,5,2 +CC038/GeniUnc,3,5,4,8,7,1,2,6 +CC039/Unc,7,3,4,2,1,6,5,8 +CC040/TauUnc,4,1,3,5,7,2,6,8 +CC041/TauUnc,1,2,4,7,8,3,6,5 +CC042/GeniUnc,7,3,5,1,6,8,4,2 +CC043/GeniUnc,2,8,1,7,5,3,6,4 +CC044/Unc,3,4,6,2,5,8,1,7 +CC045/GeniUnc,8,2,6,3,4,5,1,7 +CC046/Unc,7,3,4,5,6,8,1,2 +CC047/Unc,1,6,4,7,5,2,8,3 +CC049/TauUnc,2,8,3,1,5,4,7,6 +CC050/Unc,7,8,2,4,3,1,6,5 +CC051/TauUnc,1,2,4,7,8,5,6,3 +CC052/GeniUnc,8,7,6,3,4,2,1,5 +CC053/Unc,6,3,1,5,2,7,8,4 +CC055/TauUnc,7,1,5,8,4,6,2,3 +CC056/GeniUnc,3,8,1,7,5,4,6,2 +CC057/Unc,6,8,4,1,7,3,2,5 +CC058/Unc,3,7,4,8,5,2,1,6 +CC059/TauUnc,1,2,4,6,5,8,7,3 +CC060/Unc,5,1,6,4,7,3,8,2 +CC061/GeniUnc,4,3,5,2,8,1,7,6 +CC062/Unc,6,8,7,2,4,3,1,5 +CC063/Unc,6,8,5,2,3,4,7,1 +CC065/Unc,2,4,8,5,7,3,1,6 +CC068/TauUnc,7,1,3,5,4,6,8,2 +CC070/TauUnc,7,8,6,3,4,2,1,5 +CC071/TauUnc,3,8,4,6,7,1,5,2 +CC072/TauUnc,1,7,2,8,3,4,6,5 +CC073/Unc,2,5,1,3,8,4,6,7 +CC074/Unc,7,8,2,1,6,5,3,4 +CC075/Unc,5,2,6,7,3,8,4,1 +CC076/Unc,3,4,8,5,2,7,6,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccqtl/indiv_marker/CC_MMnGM_test/cc_geno19.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,3061 @@ +# Chromosome 19 genotypes for Collaborative Cross (CC) lines inferred from genotypes from Srivastava et al. (2017) doi:10.1534/genetics.116.198838, data at doi:10.5281/zenodo.377036 +# nrow 3057 +# ncol 70 +marker,CC001/Unc,CC002/Unc,CC003/Unc,CC004/TauUnc,CC005/TauUnc,CC006/TauUnc,CC007/Unc,CC008/GeniUnc,CC009/Unc,CC010/GeniUnc,CC011/Unc,CC012/GeniUnc,CC013/GeniUnc,CC015/Unc,CC016/GeniUnc,CC017/Unc,CC018/Unc,CC019/TauUnc,CC020/GeniUnc,CC021/Unc,CC022/GeniUnc,CC023/GeniUnc,CC024/GeniUnc,CC025/GeniUnc,CC026/GeniUnc,CC027/GeniUnc,CC028/GeniUnc,CC029/Unc,CC030/GeniUnc,CC031/GeniUnc,CC032/GeniUnc,CC033/GeniUnc,CC034/Unc,CC035/Unc,CC036/Unc,CC037/TauUnc,CC038/GeniUnc,CC039/Unc,CC040/TauUnc,CC041/TauUnc,CC042/GeniUnc,CC043/GeniUnc,CC044/Unc,CC045/GeniUnc,CC046/Unc,CC047/Unc,CC049/TauUnc,CC050/Unc,CC051/TauUnc,CC052/GeniUnc,CC053/Unc,CC055/TauUnc,CC056/GeniUnc,CC057/Unc,CC058/Unc,CC059/TauUnc,CC060/Unc,CC061/GeniUnc,CC062/Unc,CC063/Unc,CC065/Unc,CC068/TauUnc,CC070/TauUnc,CC071/TauUnc,CC072/TauUnc,CC073/Unc,CC074/Unc,CC075/Unc,CC076/Unc 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccqtl/marker_set/MMnGM_m38_test/MMnGM_foundergeno19.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,3413 @@ +# Founder genotypes (A/B/-) for combined SNPs from MegaMUGA and GigaMUGA +# nrow 3409 +# ncol 9 +marker,A,B,C,D,E,F,G,H +UNCHS047038,A,A,A,A,A,B,B,B +JAX00468911,B,B,B,B,B,B,B,A +JAX00468921,B,B,B,B,B,B,A,B +backupJAX00086312,A,A,A,A,A,B,B,B +UNCHS047039,A,A,A,A,A,B,B,B +UNCHS047040,B,B,B,B,B,B,A,B +JAX00468938,A,A,A,A,A,B,A,B +UNCHS047041,B,B,B,B,B,B,A,A +UNCHS047043,A,B,B,A,B,A,A,B +UNCHS047042,B,A,A,B,A,B,B,B +UNCHS047044,A,B,B,A,B,A,B,A +UNC190137872,A,B,B,A,B,A,-,A +B6_rs30503185,B,A,B,B,B,B,B,B +repB6_rs30503185,B,A,B,B,B,B,B,B +JAX00468967,A,A,A,A,A,B,B,B +UNCHS047045,B,A,A,B,A,B,A,B +UNCHS047046,B,A,A,B,A,B,B,B +JAX00468987,A,A,A,A,A,A,B,A +UNC29827168,B,A,A,B,A,B,A,B +UNCHS047047,B,A,A,B,A,B,B,B +UNCHS047049,A,B,B,A,B,A,-,A +UNCHS047048,A,A,A,A,A,B,A,B +UNC29827681,A,A,A,A,A,B,A,A +UNCHS047051,B,B,B,B,B,A,B,A 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccqtl/marker_set/MMnGM_m38_test/MMnGM_gmap19.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,3413 @@ +# Genetic map for combined SNPs from MegaMUGA and GigaMUGA, chromosome 19 +# nrow 3409 +# ncol 3 +marker,chr,pos +UNCHS047038,19,3.008 +JAX00468911,19,3.029 +JAX00468921,19,3.051 +backupJAX00086312,19,3.059 +UNCHS047039,19,3.097 +UNCHS047040,19,3.099 +JAX00468938,19,3.129 +UNCHS047041,19,3.155 +UNCHS047043,19,3.158 +UNCHS047042,19,3.159 +UNCHS047044,19,3.163 +UNC190137872,19,3.213 +B6_rs30503185,19,3.24 +repB6_rs30503185,19,3.24 +JAX00468967,19,3.273 +UNCHS047045,19,3.353 +UNCHS047046,19,3.356 +JAX00468987,19,3.368 +UNC29827168,19,3.376 +UNCHS047047,19,3.377 +UNCHS047049,19,3.377 +UNCHS047048,19,3.379 +UNC29827681,19,3.441 +UNCHS047051,19,3.475 +UNC29828334,19,3.527 +UNCHS047053,19,3.581 +UNC29828976,19,3.611 +UNC29829291,19,3.664 +JAX00469050,19,3.684 +JAX00469067,19,3.73 +JAX00469069,19,3.736 +JAX00469078,19,3.759 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/format-data/in_covar.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,42 @@ +Individual_ID,Mother_Line,Father_Line,Sex,testis_mean_weight,Veffect +1,CC001,CC001,M,5.818235504,-2.835143628 +10,CC016,CC016,M,3.739612593,-2.882525754 +11,CC017,CC017,M,3.422682087,0.055534678 +103,CC017,CC017,F,3.422682087,0.055534678 +104,CC017,CC017,M,3.422682087,0.055534678 +12,CC018,CC018,M,3.136692914,0.971825782 +13,CC019,CC019,M,3.573105975,0.930045911 +14,CC021,CC021,M,3.722488812,0.595834201 +15,CC024,CC024,M,5.864917353,5.881663555 +16,CC025,CC025,M,5.978850633,0.915015624 +17,CC026,CC026,M,3.34205356,0.106306062 +18,CC027,CC027,M,5.642146379,5.369760321 +19,CC028,CC028,M,3.97390515,-2.141555799 +2,CC002,CC002,M,5.936182152,5.002714702 +20,CC032,CC032,M,3.962726698,0.59975743 +21,CC035,CC035,M,3.624139599,10.54541706 +22,CC037,CC037,M,5.357227748,5.154564084 +23,CC039,CC039,M,3.083358748,10.83919268 +24,CC040,CC040,M,3.188102228,10.8149819 +25,CC041,CC041,M,5.646223938,0.027703533 +251,CC041,CC041,M,5.646223938,0.027703533 +252,CC041,CC041,F,5.646223938,0.027703533 +253,CC041,CC041,F,5.646223938,0.027703533 +26,CC042,CC042,M,3.765926534,10.30781424 +27,CC043,CC043,M,3.738827317,0.977178944 +28,CC045,CC045,M,3.223749876,-2.821486666 +29,CC049,CC049,M,3.019012501,10.10263163 +3,CC003,CC003,M,5.932263875,0.942572487 +30,CC051,CC051,M,3.315348306,0.179163174 +31,CC058,CC058,M,5.742239552,0.582790699 +32,CC059,CC059,M,3.354683834,-2.759830198 +33,CC060,CC060,M,3.011010557,0.626850016 +34,CC061,CC061,M,3.609392869,5.14990025 +35,CC071,CC071,M,5.540154046,0.678959595 +36,CC075,CC075,M,3.660978931,0.565822081 +4,CC004,CC004,M,5.766045746,0.372629597 +5,CC005,CC005,M,5.990804977,0.245475169 +6,CC006,CC006,M,3.407872526,10.24169712 +7,CC011,CC011,M,3.541614987,0.568675927 +8,CC012,CC012,M,3.188648514,10.60700532 +9,CC013,CC013,M,3.917461049,10.7388086
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/format-data/in_phenotypes.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,42 @@ +Individual_ID,Mother_Line,Father_Line,logNKnb.liver,logNKnb.lungs +1,CC001,CC001,6.506742845,7 +10,CC016,CC016,6.421386332,2 +11,CC017,CC017,5.559547877,1 +103,CC017,CC017,5.559547877,1 +104,CC017,CC017,5.559547877,1 +12,CC018,CC018,4.597236508,8 +13,CC019,CC019,4.690688705,8 +14,CC021,CC021,4.321998933,7 +15,CC024,CC024,4.887865762,3 +16,CC025,CC025,7.21148308,6 +17,CC026,CC026,5.414487739,7 +18,CC027,CC027,4.63559842,1 +19,CC028,CC028,6.223123036,4 +2,CC002,CC002,5.545145352,7 +20,CC032,CC032,3.474456226,1 +21,CC035,CC035,6.183900832,5 +22,CC037,CC037,5.925766119,5 +23,CC039,CC039,6.135258913,6 +24,CC040,CC040,4.216052096,8 +25,CC041,CC041,6.387956767,3 +251,CC041,CC041,6.387956767,3 +252,CC041,CC041,6.387956767,3 +253,CC041,CC041,6.387956767,3 +26,CC042,CC042,4.848416205,7 +27,CC043,CC043,5.62242207,1 +28,CC045,CC045,5.676811412,6 +29,CC049,CC049,4.912206141,4 +3,CC003,CC003,4.273057987,5 +30,CC051,CC051,5.895200672,6 +31,CC058,CC058,6.52004005,9 +32,CC059,CC059,4.953059546,5 +33,CC060,CC060,4.865837615,8 +34,CC061,CC061,6.611272246,1 +35,CC071,CC071,6.669919485,1 +36,CC075,CC075,5.811523296,2 +4,CC004,CC004,5.82285412,6 +5,CC005,CC005,5.141162615,4 +6,CC006,CC006,5.321079849,6 +7,CC011,CC011,4.811942569,9 +8,CC012,CC012,3.732808631,8 +9,CC013,CC013,4.992181237,5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/format-data/only-female-covar.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,225 @@ +Individual_ID,Mother_Line,Father_Line,Sex +1,CC039,CC039,F +10,CC037,CC037,F +100,CC006,CC006,F +101,CC006,CC006,F +102,CC016,CC016,F +103,CC016,CC016,F +104,CC016,CC016,F +105,CC016,CC016,F +106,CC025,CC025,F +107,CC025,CC025,F +108,CC025,CC025,F +109,CC040,CC040,F +11,CC037,CC037,F +110,CC040,CC040,F +111,CC040,CC040,F +112,CC040,CC040,F +113,CC041,CC041,F +114,CC041,CC041,F +115,CC041,CC041,F +116,CC049,CC049,F +117,CC049,CC049,F +118,CC049,CC049,F +119,CC043,CC043,F +12,CC037,CC037,F +120,CC043,CC043,F +121,CC005,CC005,F +122,CC005,CC005,F +123,CC005,CC005,F +124,CC019,CC019,F +125,CC019,CC019,F +126,CC024,CC024,F +127,CC024,CC024,F +128,CC024,CC024,F +129,CC018,CC018,F +13,CC012,CC012,F +130,CC018,CC018,F +131,CC035,CC035,F +132,CC035,CC035,F +133,CC035,CC035,F +134,CC035,CC035,F +135,CC060,CC060,F +136,CC060,CC060,F +137,CC060,CC060,F +138,CC042,CC042,F +139,CC042,CC042,F +14,CC012,CC012,F +140,CC042,CC042,F +141,CC004,CC004,F +142,CC004,CC004,F +143,CC004,CC004,F +144,CC016,CC016,F +145,CC016,CC016,F +146,CC016,CC016,F +15,CC012,CC012,F +151,CC004,CC004,F +152,CC004,CC004,F +153,CC004,CC004,F +154,CC004,CC004,F +155,CC001,CC001,F +156,CC001,CC001,F +157,CC001,CC001,F +158,CC006,CC006,F +159,CC006,CC006,F +16,CC012,CC012,F +160,CC006,CC006,F +161,CC006,CC006,F +162,CC012,CC012,F +163,CC012,CC012,F +164,CC012,CC012,F +165,CC032,CC032,F +166,CC032,CC032,F +167,CC032,CC032,F +168,CC002,CC002,F +169,CC002,CC002,F +17,CC018,CC018,F +170,CC002,CC002,F +171,CC051,CC051,F +172,CC051,CC051,F +173,CC051,CC051,F +174,CC061,CC061,F +175,CC061,CC061,F +176,CC061,CC061,F +177,CC071,CC071,F +178,CC071,CC071,F +179,CC071,CC071,F +18,CC018,CC018,F +180,CC071,CC071,F +181,CC027,CC027,F +182,CC027,CC027,F +183,CC027,CC027,F +184,CC024,CC024,F +185,CC024,CC024,F +186,CC005,CC005,F +187,CC005,CC005,F +188,CC042,CC042,F +189,CC039,CC039,F +19,CC018,CC018,F +190,CC032,CC032,F +191,CC032,CC032,F +196,CC005,CC005,F +197,CC005,CC005,F +198,CC059,CC059,F +199,CC059,CC059,F +2,CC039,CC039,F +20,CC018,CC018,F +200,CC059,CC059,F +201,CC059,CC059,F +202,CC027,CC027,F +203,CC035,CC035,F +204,CC035,CC035,F +205,CC035,CC035,F +206,CC032,CC032,F +207,CC032,CC032,F +208,CC019,CC019,F +209,CC028,CC028,F +21,CC013,CC013,F +210,CC040,CC040,F +211,CC071,CC071,F +212,CC071,CC071,F +219,CC024,CC024,F +22,CC013,CC013,F +220,CC024,CC024,F +221,CC040,CC040,F +222,CC040,CC040,F +223,CC003,CC003,F +224,CC003,CC003,F +225,CC003,CC003,F +226,CC003,CC003,F +227,CC026,CC026,F +228,CC026,CC026,F +229,CC026,CC026,F +23,CC013,CC013,F +230,CC026,CC026,F +231,CC026,CC026,F +232,CC026,CC026,F +233,CC045,CC045,F +234,CC045,CC045,F +235,CC045,CC045,F +236,CC045,CC045,F +237,CC045,CC045,F +238,CC045,CC045,F +24,CC013,CC013,F +25,CC059,CC059,F +26,CC059,CC059,F +27,CC059,CC059,F +28,CC042,CC042,F +29,CC042,CC042,F +3,CC039,CC039,F +30,CC042,CC042,F +31,CC017,CC017,F +32,CC017,CC017,F +33,CC017,CC017,F +34,CC028,CC028,F +35,CC028,CC028,F +36,CC028,CC028,F +37,CC028,CC028,F +38,CC041,CC041,F +39,CC041,CC041,F +4,CC039,CC039,F +40,CC041,CC041,F +41,CC041,CC041,F +42,CC075,CC075,F +43,CC075,CC075,F +44,CC075,CC075,F +45,CC013,CC013,F +46,CC013,CC013,F +47,CC013,CC013,F +48,CC061,CC061,F +49,CC061,CC061,F +5,CC019,CC019,F +50,CC061,CC061,F +51,CC061,CC061,F +52,CC025,CC025,F +53,CC025,CC025,F +54,CC025,CC025,F +55,CC025,CC025,F +56,CC043,CC043,F +57,CC043,CC043,F +58,CC043,CC043,F +59,CC043,CC043,F +6,CC019,CC019,F +60,CC049,CC049,F +61,CC049,CC049,F +62,CC049,CC049,F +63,CC049,CC049,F +64,CC001,CC001,F +65,CC001,CC001,F +66,CC001,CC001,F +67,CC001,CC001,F +68,CC017,CC017,F +69,CC017,CC017,F +7,CC019,CC019,F +70,CC017,CC017,F +71,CC017,CC017,F +72,CC003,CC003,F +73,CC003,CC003,F +74,CC003,CC003,F +75,CC003,CC003,F +76,CC002,CC002,F +77,CC002,CC002,F +78,CC002,CC002,F +79,CC002,CC002,F +8,CC019,CC019,F +80,CC051,CC051,F +81,CC051,CC051,F +82,CC051,CC051,F +83,CC051,CC051,F +84,CC075,CC075,F +85,CC075,CC075,F +86,CC075,CC075,F +87,CC075,CC075,F +88,CC060,CC060,F +89,CC060,CC060,F +9,CC037,CC037,F +90,CC060,CC060,F +91,CC060,CC060,F +92,CC037,CC037,F +93,CC037,CC037,F +94,CC037,CC037,F +95,CC037,CC037,F +96,CC027,CC027,F +97,CC027,CC027,F +98,CC027,CC027,F +99,CC006,CC006,F
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/format-data/only-female-pheno.csv Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,225 @@ +Individual_ID,Mother_Line,Father_Line,BW_D21,ELISA_Titer +1,CC039,CC039,21.5,10.16955405 +10,CC037,CC037,24.0,11.24343451 +100,CC006,CC006,18.8,3.26814274683144 +101,CC006,CC006,22.9,7.18100985752549 +102,CC016,CC016,21.2,11.5729711165263 +103,CC016,CC016,22.0,22.2618887375923 +104,CC016,CC016,23.7,15.4612399146949 +105,CC016,CC016,20.8,13.6730484168229 +106,CC025,CC025,20.3,22.4603871684595 +107,CC025,CC025,22.1,27.4164861198956 +108,CC025,CC025,18.5,26.3012446974897 +109,CC040,CC040,30.6,7.98304568043694 +11,CC037,CC037,22.2,5.169516019 +110,CC040,CC040,31.3,11.3401993424102 +111,CC040,CC040,34.0,17.2695993106771 +112,CC040,CC040,32.4,16.3300236469837 +113,CC041,CC041,20.1,0.01 +114,CC041,CC041,23.0,0.01 +115,CC041,CC041,23.6,0.01 +116,CC049,CC049,22.7,13.7191312206798 +117,CC049,CC049,19.0,5.07915308600525 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ccqtl.loc.sample Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,7 @@ +# <unique_build_id> <dbkey> <display_name> <build> <doi> <description> <optional_description> <file_base_path> + +# CC_MMnGM indiv_marker CC_MMnGM m38 individual genotypes of each CC mouse at each marker and the funnel codes if applicable. (mega muga and giga muga) tool-data/ccqtl/indiv_marker/CC_MMnGM_ref +# MMnGM_m38 marker_set MMnGM_m38 m38 https://figshare.com/articles/dataset/MMnGM_processed_files_zip/5404762/2 Marker set for mega muga and giga muga tool-data/ccqtl/marker_set/MMnGM_m38 +# MM_m38 marker_set MM_m38 m38 https://figshare.com/articles/dataset/MM_processed_files_zip/5404750/2 Marker set for mega muga tool-data/ccqtl/marker_set/MM_m38 +# cc_variants_m38 cc_variants CC founders variants m38 m38 10.6084/m9.figshare.5280229.v3 DNA seq variants segregating among the founders tool-data/ccqtl/annotations/m38/cc_variants.sqlite +# mouse_genes_mgi_m38 genes Mouse genes mgi m38 m38 10.6084/m9.figshare.5286019.v8 gene annotation, subsetted to MGI annot tool-data/ccqtl/annotations/m38/mouse_genes_mgi.sqlite \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as +changed in revision 4550:535d276c92bc--> +<tables> + <table name="ccqtl" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, build, doi, description, optional_description, path</columns> + <file path="tool-data/ccqtl.loc" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jun 30 14:18:58 2023 +0000 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as +changed in revision 4550:535d276c92bc--> +<tables> + <table name="ccqtl" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, build, doi, description, optional_description, path</columns> + <file path="${__HERE__}/test-data/ccqtl.loc" /> + </table> +</tables> \ No newline at end of file