Mercurial > repos > malex > bayesase
diff summarize_sam_compare_cnts_table_1cond.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/summarize_sam_compare_cnts_table_1cond.xml Thu Jan 14 21:51:36 2021 +0000 @@ -0,0 +1,155 @@ +<tool id="summarize_sam_compare_cnts_table_1cond" name="Summarize and Filter ASE Count Tables" version="21.1.13"> + <description>based on user-defined APN threshold</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + mkdir outputs; + cd outputs; + summarize_sam_compare_cnts_table_1cond.py + --design=$design + --collection_identifiers="${",".join($collection.keys())}" + --collection_filenames="${",".join(map(str, $collection))}" + --parent1=$parent1 + --parent2=$parent2 + --sampleCol=$sampleCol + --sampleIDCol=$sampleIDCol + --apn=$apn + --out=`pwd` +]]></command> + <inputs> + <param name="design" type="data" format="tabular,tsv" label="Sample Design file" help="Select the Sample Design File - this can be created with the Combine ASE Counts Tables tool."/> + <param name="collection" type="data_collection" collection_type="list" label="Collection of Combined ASE Count Tables" help="Select the collection containing ASE Count Tables combined (summed) across technical replicates."/> + <param name="parent1" type="text" label="Updated genome 1 (G1)" value="G1" help="Enter the name of the column in the design file for genome 1 (e.g. G1)" /> + <param name="parent2" type="text" label="Updated genome 2 (G2)" value="G2" help="Enter the name of the column in the design file for genome 2 (e.g. G2)" /> + <param name="sampleIDCol" type="text" value="sampleID" label="Sample ID Column" help="Enter the name of the column in the design file containing sampleIDs" /> + <param name="sampleCol" type="text" value="comparate" label="Comparate Column" help="Enter the header name of the column in design file containing comparate names"/> + <param name="apn" type="text" label="APN (Average Reads per Nucleotide) threshold" value="5" help="Enter an APN threshold value for flagging a feature as 'expressed'. The default setting is 5."/> + </inputs> + <outputs> + <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Summarized and Filtered ASE Counts table"> + <discover_datasets pattern="(?P<name>ase.*)" ext="tabular" sort_by="reverse_filename" directory="outputs" /> + </collection> + </outputs> + <tests> + <test> + <param name="design" value="BASE_testdata/summarize_counts_testdata/summarization_df_BASE.tabular" ftype="tabular"/> + <param name="collection" value="BASE_testdata/summarize_counts_testdata/combined_ASE_counts_tables_BASE" ftype="data_collection"/> + <param name="parent1" value="G1" ftype="text"/> + <param name="parent2" value="G2" ftype="text"/> + <param name="sampleIDcol" value="sampleID" ftype="text"/> + <param name="samplecol" value="comparate" ftype="text"/> + <param name="apn" value="1" ftype="text"/> + <output_collection name="split_output" type="list"> + <element name="FEATURE_ID"> + <assert_contents> + <has_text_matching expression="Summarize_ASE_counts_test_data"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**Tool Description** + +The Summarize SAM Compare Counts tool filters data based on whether or not they meet the requirements for input into the Bayesian module to test for allelic specific expression. +Using the Sample Design File, it creates one file with all the biological replicates for a given comparate. +The data are then filtered, removing features that don't meet a user-defined APN (average number of reads per nucleotide) threshold, which inicates whether or not a feature is expressed by having high read coverage. + +The default APN threshold value is 5. Features that do not meet this cutoff are considered to have insufficient information needed to estimate model parameters. + +For each feature, if at least 1 replicate in a comparate has an APN value greater than the user-specified cutoff value then the binary indicator flag in the output (flag_analyze) will be equal to 1, else equal to 0. + + +**INPUTS** + +**Sample Design File [REQUIRED]** + +The design file must contain the sampleIDs for the summed count table. This sampleID must contain the biological replicate number that the summed ASE Counts table are aggregates of. + +The comparate column contains the names of the comparates and their conditions. It can contain the same information as the sampleID but excludes the biological replicate number. + +**TIP**: The Sample Design file can be created using the *Combine Counts Table* tool. + +An example Sample Design File: + + G1 G2 sampleID comparate + W1118 W55 W55_M_rep1 W55_M + W1118 W55 W55_M_rep2 W55_M + W1118 W55 W55_V_rep1 W55_V + W1118 W55 W55_V_rep2 W55_V + + +**Collection of Summed ASE Counts Tables [REQUIRED]** + +Input the collection of summed ASE counts table created by the Combine Counts Tables tool. + +Example input ASE Counts Table: + + +------------+-------------------+-------------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ + |Feature_ID |APN_both |APN_total_reads | BOTH_EXACT |BOTH_INEXACT_EQUAL|SAM_A_ONLY_EXACT|SAM_B_ONLY_EXACT| SAM_A_EXACT_SAM_B_INEXACT|SAM_B_EXACT_SAM_A_INEXACT|SAM_A_ONLY_SINGLE_INEXACT|SAM_B_ONLY_SINGLE_INEXACT |SAM_A_INEXACT_BETTER|SAM_B_INEXACT_BETTER| + +============+===================+===================+============+==================+================+================+==========================+=========================+=========================+==========================+====================+====================+ + | l(1)G0196 |10.255101044615834 |12.723420872791175 | 721 |1476 |120 |173 |0 | 2 |96 |136 |0 |2 | + +------------+-------------------+-------------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ + | CG8920 |7.0372442219932285 |8.62888267334020 | 207 |293 |31 |62 |0 | 0 |8 |12 |0 |0 | + +------------+-------------------+-------------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ + + +**Header names [REQUIRED]** +Type in the designated names of the following columns in the design file: + + (1) Genome 1 - the name of the column containing updated genome 1 (eg G1) + (2) Genome 2 - the name of the column containing updated genome 2 (eg G2) + (3) SampleID Column - the name of the column containing the sampleIDs + (4) Comparate Column - the name of the column containing comparate information + +**APN Threshold [REQUIRED]** + +Specify an APN threshold for flagging features as 'expressed'. Features that do not meet this threshold are considered to have coverage and will not be included in the Bayesian analysis. + +**NOTE**: The default setting is 5. + + +**OUTPUTS** + + +**This tool outputs the following:** + +(1) For each comparate, a summary TSV file containing the flagged indicators recording whether or +not a feature meets the specified APN threshold. In the below column header descriptions, +{comparate} refers tothe comparate in the Sample Design File (e.g. W55_M). The number of columns +generated is dependent on the number of replicates. + +The first three rows of an example output 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 0 2 0 0 3 0 0.253164557 0.253164557 0 0 0 0 0 0 + CG8920 W1118 W55 0 2 0 0 2 0 0.660066007 0.660066007 0 0 0 0 0 0 + CG10932 W1118 W55 0 2 0 0 0 0 0 0 0 0 0 0 0 0 + +In the example output above, the features have low read counts and they do not surpass the default APN threshold of 5 (APN threshold can be changed by user), therefore the flag_analyze variable=0, and the features would be excluded from Bayesian Analysis. + +Column header definitions:: + + ◦ {comparate}_flag_analyze: 0/1 binary indicator flag where a “1” means that at least one replicate for the indicated comparate has an APN greater than the user-specified cutoff value. + ◦ {comparate_n}_num_reps: The amount of replicates for the indicated comparate. + ◦ counts_{comparate}_g1_total_{replicate_number}: Total number of unique reads from a given replicate that mapped to updated parental genome 1 + ◦ counts_{comparate}_g2_total_{replicate_number}: Total number of unique reads from a given replicate that mapped to updated parental genome 2 + ◦ counts_{comparate}_both_total_{replicate_number}: Total number of unique reads from a given replicate that mapped equally well to both updated parental genomes + ◦ {comparate}_flag_apn_{replicate_number}: 0/1 flag where a “1” indicates that the APN value for a given feature is above the user-defined APN threshold + ◦ {comparate}_total_reads_APN_{replicate_number}: The calculated APN value for the total number of unique reads that mapped to a given feature + ◦ {comparate}_both_APN_{replicate_number}: The calculated APN value for the number of unique reads that mapped equally well to both updated parental genomes for a given feature + + + ]]></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> +