annotate calculate_priors_from_ase_count_tables.xml @ 0:e979cb57a5d5 draft default tip

"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"

<tool id="calculate_priors_from_ase_count_tables" name="Calculate Prior Probability Estimates" version="21.1.13">
    <description>using ASE Count Tables</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
    mkdir outputs;
    cd outputs;
    calculate_priors_ase_count_tables.py
    --output=`pwd`
    --design=$design
    --collection_identifiers="${",".join($collection.keys())}"
    --collection_filenames="${",".join(map(str, $collection))}"

]]></command>
    <inputs>
        <param name="design" type="data" format="tabular,tsv" label="Priors Design File" help="Select the Priors Design file [created by the Reformat Sample Design File Tool]"/>
        <param name="collection" type="data_collection" collection_type="list" label="Select dataset collection for Prior Calculations" help="Datasets in this collection can be generated from simulated or DNA reads using the Align and Count' and 'Summarize counts' Workflows."/>
    </inputs>
    <outputs>
      <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Calculate Prior Probabilities">
        <discover_datasets pattern="(?P&lt;designation&gt;.*)" ext="tsv" directory="outputs"/>
      </collection>
    </outputs>
    <tests>
        <test>
            <param name="design" value="summarize_counts_testdata/sample_design_file.tabular" ftype="tsv"/>
            <param name="collection">
              <collection type="list">
                <element name="FEATURE_ID" value="summarize_counts_testdata/filtered_ASE_counts_tables_BASE"/>
              </collection>
             </param>
             <output_collection name="split_output" type="list">
               <element name="FEATURE_ID">
                 <assert_contents>
                   <has_text_matching expression="Calculated_priors" />
                  </assert_contents>
                </element>
              </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**Tool Description**

The Calculate Prior Probability Estimates tool calculates prior probability estimates for each of the comparates.
Prior Probability is a part of Bayesian statistical inference, and is useful for ruling out whether alleles aligning better to one parent is due to allelic imbalance,
or if it is really due to mapping biases or technical errors in the data.

The output file contains computations for three variables, prior_[comparate name]_g1 and prior_[comparate name]_g2, which represent the probability that the feature will align to either parental genome, and prior_[comparate name]_both, which are the chances the feature will align to equally well to both genomes.


Calculation::

    prior_{comparate)_both= [# reads aligning equally to both genomes]                prior_{comparate)_{G1/G2}= 1-(prior_both)
                 -----------------------------------------                                                        --------------
                      [total uniquely mapped reads]                                                                      2




--------------------------------------------------------------------------------------------------------------------

**Inputs**

**Prior Design File [REQUIRED]**

(1) This tool requires the Priors Design file, which can be created using the *Reformat Sample Design File* tool.

The Priors Design File must be in the following format and contain the correct header order:

1. G1- This is the name of the paternal genome
2. G2- The name of the maternal genome
3. comparate - contains comparate conditions. Exclude replicate number.



Example of input design file::

    +-------+------+-----------+
    |   G1  |  G2  | comparate |
    +-------+------+-----------+
    | W1118 |  W55 | W55_M     |
    +-------+------+-----------+
    | W1118 |  W55 | W55_M     |
    +-------+------+-----------+


**Input for Priors Calculations - Summed ASE Counts Tables [Required]**

The collection of datasets in Summarized and Filtered Format.
These datasets can be generated by running simulated reads or DNA reads through the 'Align and Count' and 'Summarize Counts' Workflows.

Example Input File::

	FEATURE_ID	g1	g2	W55_M_flag_analyze     W55_M_num_reps   	W55_M_g1_total_rep1     	W55_M_g2_total_rep1     	W55_M_both_total_rep1       	W55_M_flag_apn_rep1     	W55_M_APN_total_reads_rep1	W55_M_APN_both_rep1	W55_M_g1_total_rep2     	W55_M_g2_total_rep2     	W55_M_both_total_rep2   	W55_M_flag_apn_rep2     	W55_M_APN_total_reads_rep2      	W55_M_APN_both_rep2
	l(1)G0196	W1118	W55	1    			2			691				519				5020 	        		1   				29.073464805232			23.4243873865079		1075				812				7481				1			43.7266913990042		34.9168212437762
	CG8920  	W1118	W55  	1			2			29				 62				 647    			1				10.3878993081113		9.10716914470779		38				126				920				1			15.2470189901369		12.9534815250994
	CG10932 	W1118	W55 	1			2			163				122		                1112		    		1				89.9299663299663		71.5858585858586		237				134				1881				1			144.974410774411		121.086195286195



----------------------------------------------------------------------------------------------------

**Tool Outputs**

-One TSV file containing the calculated prior probabilities for reads that align preferentially to G1, G2, and those that align equally to both.

Example Priors Calculation File::

    +--------------+------------------+-----------------+---------------+
    | FEATURE_ID   | prior_W55_M_both | prior_W55_M_g1  |prior_W55_M_g2 |
    +==============+==================+=================+===============+
    | l(1)G0196    | 0.799907266902   | 0.1183611532625 | 0.08173157983 |
    +--------------+------------------+-----------------+---------------+
    | CG10932      | 0.853881278538   | 0.0597412480974 | 0.08637747336 |
    +--------------+------------------+-----------------+---------------+
    | CG8920       | 0.80895522388    | 0.1233830845771 | 0.06766169154 |
    +--------------+------------------+-----------------+---------------+
    | Mapmodulin   | 0.8987341772151  | 0.0855389336401 | 0.01572688914 |
    +--------------+------------------+-----------------+---------------+

Header descriptions::

    prior_{comparate}_both: prior probability estimate for the total number of reads that mapped equally well to both updated parental genomes
    prior_{comparate}_g1: prior probability estimate for the total number of reads that mapped to updated parental genome 1
    prior_{comparate}_g2: prior probability estimate for the total number of reads that mapped to updated parental genome 2


    ]]></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>