Mercurial > repos > malex > bayesase
diff NBmodel_stan2_galaxy.xml @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
| author | malex |
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| date | Thu, 14 Jan 2021 21:51:36 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NBmodel_stan2_galaxy.xml Thu Jan 14 21:51:36 2021 +0000 @@ -0,0 +1,198 @@ +<tool id="NBmodel_stan2_galaxy" name="Run the Bayesian model" version="21.1.13"> + <description>nbmodel_stan2_flex_prior.R</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <stdio> + <exit_code range="1:" level="fatal" /> + <regex match="recommend" + source="stderr" + level="warning" + description="recomendation message was written in stderr" /> + <regex match="Loading library" + source="stderr" + level="log" /> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> + <command><![CDATA[ + nbmodel_stan2.py + --design=$design + --infile=$infile + --outfile=$output + --cond=$cond + --iterations=$iterations + --warmup=$warmup + +]]></command> + <inputs> + <param name="design" type="data" format="tabular,tsv" label="Design File" help="Select your Comparate Design File."/> + <param name="infile" type="data" format="tabular,tsv" label="Input File" help="Select the dataset with the merged comparates and new headers."/> + <param name="cond" type="text" label="conditions" value="2" help="Enter the number of conditions your're comparing (e.g. M v F would be 2)"/> + <param name="iterations" type="text" label="iterations" value="100000" help="Enter the number of iterations [default = 100000]"/> + <param name="warmup" type="text" label="warmup" value="10000" help="Enter the warmup number [default = 10000]"/> + </inputs> + <outputs> + <data name="output" format="tsv" label="${tool.name} on ${on_string}: Bayesian Model Output" /> + </outputs> + <tests> + <test> + <param name="design" ftype="data" value="bayesian_input/comparate_design_file.tsv"/> + <param name="infile" ftype="data" value="bayesian_input/bayesian_input_W55_M_V.tabular"/> + <param name="cond" ftype="text" value="2" /> + <param name="iterations" ftype="text" value="100000" /> + <param name="warmup" ftype="text" value="10000" /> + <output name="output" file="bayesian_output_W55_M_V.tabular" /> + </test> + </tests> + <help><![CDATA[ + +**Tool Description** + +The Run the Bayesian model tool sets the parameters for the NBModel, generalizes the input and output name requirements and initiates the STAN implementation of the NBModel. +The statistical model is packaged in the script environmentalmodel2.stan (supported on the STAN platform) and wrapped in the R script (nbmodel_stan2_flex_prior.R). +Th original R script has hardcoded the names of the conditions used in the original implementation. + +The model is used to test three hypotheses of interest: + for i = 1,2 and k = 1,2,…,Ki. + Allelic balance in Comparate 1 (e.g., Male) or, equivalently, H01: α1 = 1. + Allelic balance in Comparate 2 (e.g., Female), H02: α2 = 1. + The level of AI is not different between comparates. + +If either H01 or H02 are rejected, (at a threshold of posterior p-value 0.05) “AI_{cn }_decision” , where n refers to the comparate number, is set to 1. +If either of these cannot be rejected, these column values remain 0. + +Testing the third null hypothesis tests determines if the true proportion of reads coming from G1 is the same within Comparate 1 as it is within Comparate 2 (Novelo et. al 2018). +This is a separate process that effectively tests if α1 = α2. If H03 is rejected, the Bayesian model output columns “AI_diffinc2andc1” =1. +All model output is compiled into one wide format TSV file per Bayesian input file. + + +**Inputs** + + +**Comparate Design File [REQUIRED]** + +**NOTE**:The Comparate Design File is created and supplied by the user. It explicitly lists the comparates that the user wants to compare. + +The Comparate Design File must contain the following columns, in order:: + + (1) Comparate_1: comparate 1 identifier (ex. W55_M) + (2) Comparate_2: comparate 2 identifier (ex. W55_V) + (3) CompID: An unique identifier that specifies the condition (ex. W55_M_V) + +Example Comparate Design File: + + +---------------+---------------+----------+ + | Comparate_1 | Comparate_2 | compID | + +---------------+---------------+----------+ + | R105_F | R105_M | R105_F_M | + +---------------+---------------+----------+ + + +**Dataset or Collection of Datasets containing Comparates for comparisons[REQUIRED]** + +These files can be generated by the "Merge Comparate Datasets and Generate Headers tool. + +Example Input File + + +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ + | Feature_ID | prior_c1_both | prior_c1_g1 | prior_c1_g2 | c1_flag_analyze | c1_num_reps | c1_g1_total_rep1 | c1_g2_total_rep1 | c1_both_total_rep1 | c1_flag_apn_rep1 | c1_APN_total_reads_rep1 | c1_APN_both_rep1 | c1_g1_total_rep2 | c1_g2_total_rep2 | c1_both_total_rep2 | c1_flag_apn_rep2 | c1_APN_total_reads_rep2 | c1_APN_both_rep2 |prior_c2_both | prior_c2_g1 | prior_c2_g2 | c2_flag_analyze | c2_num_reps | c2_g1_total_rep1 | c2_g2_total_rep1 | c2_both_total_rep1 | c2_flag_apn_rep1 | c2_flag_apn_rep1 | c2_APN_both_rep1 | c2_g1_total_rep2| c2_g2_total_rep2 | c2_both_total_rep2 | c2_flag_apn_rep2 | c2_APN_total_reads_rep2 | c2_APN_both_rep2 | + +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ + |l(1)G1096 |0.799907266902715| 0.118361153262519 | 0.0817315798347665 | 1 | 2 | 295 | 234 | 2197 | 1 | 12.7234208727912 | 10.2551010446158 | 1885 | 1165 | 12201 | 1 | 71.2019427901982 | 56.9617787757493 | 0.802196053469128 | 0.114417568427753 | 0.0833863781031191 | 1 | 2 | 691 | 519 | 5020 | 1 | 29.0734648052328 | 23.4243873865079 | 1075 | 812 | 7481 | 1 | 43.7266913990042 | 34.9168212437762 | + +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ + | CG10932 |0.853881278538813| 0.0597412480974125| 0.0863774733637747 | 1 | 2 | 13 | 39 | 308 | 1 | 5.06815839835124 | 4.33534520830266 | 100 | 134 | 1394 | 1 | 22.9213896658325 | 19.6266745178861 | 0.866028708133971 | 0.0344497607655502| 0.0995215311004785 | 1 | 2 | 29 | 62 | 674 | 1 | 10.3878993081113 | 9.10716914470779 | 38 | 125 | 920 | 1 | 15.2470189901369 | 12.9534815250994 | + +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ + | CG8920 |0.808955223880597| 0.123383084577114 | 0.0676616915422886 | 1 | 2 | 93 | 20 | 500 | 1 | 39.4720538720539 | 32.1912457912458 | 347 | 257 | 2633 | 1 | 208.422222222222 | 169.53063973064 | 0.821591948764867 | 0.108417200365965 | 0.0699908508691674 | 1 | 2 | 163 | 122 | 1112 | 1 | 89.9299663299663 | 71.5858585858586 | 237 | 134 | 1881 | 1 | 144.974410774411 | 121.086195286195 | + +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ + +------------------------------------------------------------------------------------------------------ + +**Output** + + +The tool generates a single TSV for every comparison (row) in the Comparate Design File: + + +Example Bayesian Output file: + + +-------------+------------+----------------+-----------------+------------------+------------------+----------------------+------------------+-----------------+-------------------+----------------------+--------------------+---------------------+------------------+----------------------------------+--------------------+-----------------+---------------+--------------+---------------------+--------------------+--------------------+---------------+--------------+----------------+---------------------+---------------------+----------------+-----------------+--------------+ + | comparison |FEATURE_ID | W55_M_num_reps | W55_V_num_reps | counts_W55_M_g1 | counts_W55_M_g2 | counts_W55_M_both | counts_W55_V_g1 | counts_W55_V_g2 | counts_W55_V_both | prior_W55_M_g1 |prior_W55_M_g2 |prior_W55_V_g1 | prior_W55_V_g2 | H3_independence_Bayesian_pvalue |g1_W55_M_sampleprop | g1_W55_M_theta |g1_W55_M_q025 |g1_W55_M_q975 | g1_W55_M_Bayes_pval |g1_W55_M_AI_decision|g1_W55_V_sampleprop |g1_W55_V_theta |g1_W55_V_q025 | g1_W55_V_q975 | g1_W55_V_Bayes_pval |g1_W55_V_AI_decision |alpha1_postmean | alpha2_postmean | flaganalyze | + +=============+============+================+=================+==================+==================+======================+==================+=================+===================+======================+====================+=====================+==================+==================================+====================+=================+===============+==============+=====================+====================+====================+===============+==============+================+=====================+=====================+================+=================+==============+ + | W55_M_V | l(1)G0196 | 3 | 3 | 362 | 520 | 3990 | 413 | 605 | 4475 | 0.0743021346469622 |0.106732348111658 |0.0751866011287093 |0.110140178408884 |0.866 |0.4104 |0.4948 |0.3778 |0.612 |0.9284 | 0 | 0.4057 |0.5082 | 0.3912 | 0.6231 | 0.8839 | 0 | 1.0182 | 0.9905 | 1 | + +-------------+------------+----------------+-----------------+------------------+------------------+----------------------+------------------+-----------------+-------------------+----------------------+--------------------+---------------------+------------------+----------------------------------+--------------------+-----------------+---------------+--------------+---------------------+--------------------+--------------------+---------------+--------------+----------------+---------------------+---------------------+----------------+-----------------+--------------+ + | W55_M_V | CG10932 | 3 | 3 | 45 | 79 | 661 | 91 | 101 | 723 | 0.0573248407643312 |0.100636942675159 |0.0994535519125683 |0.110382513661202 |00.5916 |0.3629 |0.5006 |0.3518 |0.6487 |0.993 | 0 |0.474 |0.4446 | 0.3019 | 0.5949 | 0.4525 |0 | 1.0108 | 1.1341 | 1 | + +-------------+------------+----------------+-----------------+------------------+------------------+----------------------+------------------+-----------------+-------------------+----------------------+--------------------+---------------------+------------------+----------------------------------+--------------------+-----------------+---------------+--------------+---------------------+--------------------+--------------------+---------------+--------------+----------------+---------------------+---------------------+----------------+-----------------+--------------+ + | W55_M_V | CG8920 | 3 | 3 | 49 | 18 | 336 | 41 | 25 | 337 | 0.121588089330025 |0.0446650124069479 |0.101736972704715 |0.0620347394540943|0.8316 |0.7313 |0.5274 |0.3786 |0.6721 |0.7099 | 0 |0.6212 |0.5057 | 0.3621 | 0.6482 | 0.9345 |0 | 0.9566 | 0.9996 | 1 | + +-------------+------------+----------------+-----------------+------------------+------------------+----------------------+------------------+-----------------+-------------------+----------------------+--------------------+---------------------+------------------+----------------------------------+--------------------+-----------------+---------------+--------------+---------------------+--------------------+--------------------+---------------+--------------+----------------+---------------------+---------------------+----------------+-----------------+--------------+ + | W55_M_V | Mapmodulin | 3 | 3 | 23 | 136 | 1553 | 15 | 188 | 1912 | 0.0134345794392523 |0.0794392523364486 |0.00709219858156028 |0.0888888888888889|0.8649 |0.1447 |0.4709 |0.3396 |0.6084 |0.6644 |0 |0.0739 |0.4552 |0.3175 | 0.602 | 0.5348 |0 | 1.0717 | 1.1083 | 1 | + +-------------+------------+----------------+-----------------+------------------+------------------+----------------------+------------------+-----------------+-------------------+----------------------+--------------------+---------------------+------------------+----------------------------------+--------------------+-----------------+---------------+--------------+---------------------+--------------------+--------------------+---------------+--------------+----------------+---------------------+---------------------+----------------+-----------------+--------------+ + + +Headers: + + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + | Name | Description | + +=====================================+==================================================================================================+ + | Comparison | • comparison being tested | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + | FEATURE_ID | • Unique genic feature ID | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + | c1_num_reps | • Number of replicates for comparate_1 | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + | c2_num_reps | • Number of replicates for comparate 2 | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |counts_{comparate}_{g1/g2} | • Number of reads that aligned preferentially to G1 (or G2) for indicated comparate | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |counts_{comparate}_both | • Number of reads that aligned equally well to both updated genomes for indicated comparate | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + | prior_{comparate}_{g1/g2} | • The prior probability that a given read will map to G1 (or G2) for {comparate} | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |H3_independence_Bayesian_evidence | • Bayesian evidence for testing the null that the alleles are independent variables. | + | | Minimum value of ev such that the 1−ev central credible interval for α1−α2. | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_sampleprop | • The sample proportion of reads among the reads mapped to G1 or G2 (but not both) that have | + | | mapped preferentially to G1 within {comparate}. | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_theta | • The point estimate of the proportion generated by G1 after adjusting for systematic bias in | + | | {comparate}. This proportion different from 1/2 implies AI in the comparate. Since | + | | {comparate}_theta is an estimate of θn1, credible intervals for θn1 are used to flag the | + | | comparate as in AI or not. | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_q025 | • Lower bound for the 95% central credible interval, or equivalently, the 2.5% quantile of the | + | | posterior distribution of θ1 | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_q975 | • Upper bound for the 95% central credible interval, or equivalently, the 97.5% quantile of | + | | the posterior distribution of θ(n1) | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_Bayes_evidence | • The Bayesian evidence. Smaller values can lead to rejection of the null. "ev" is the smallest | + | | value such that the 1−ev central credible interval for θ(n1) does not contain the value | + | | θ(n1) = 1/2, that implies allelic balance in comparate n. | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |{comparate}_AI_decision | • A 0/1 flag where a "1" indicates that the Bayesian evidence was less than 0.05 | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |alpha_postmean | • Alpha value for comparate 1, θ(1,1)!=0.5. Indicator of allelic imbalance. | + | | α1 = sqrt ((1/ Θi) – 1) | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |alpha2_postmean | • Alpha value for comparate θ(1,2) != 0.5 indicator of allelic imbalance. | + | | α2 = sqrt ((1/ Θi) – 1) | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + |flagAnalyze | • 0/1 flag where a "1" indicates that the {comparate}_flag_analyze variables going into the | + | | model were BOTH equal to 1. | + +-------------------------------------+--------------------------------------------------------------------------------------------------+ + ]]></help> + <citations> + <citation type="bibtex">@ARTICLE{Miller20BASE, + author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre}, + title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, + journal = {????}, + year = {submitted for publication} + }</citation> + </citations> +</tool>