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"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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<tool id="base_gen_headers_one_comparate" name="Generate Headers" version="21.1.13"> <description>for one condition to test for Allelic Imbalance</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command><![CDATA[ mkdir outputs; cd outputs; gen_headers_after_merge_priors_one_comparate.py --output=`pwd` --collection_identifiers="${','.join($collection.keys())}" --collection_filenames="${",".join(map(str, $collection))}" --design=$design ]]></command> <inputs> <param name="collection" type="data_collection" collection_type="list" label="Collection from Merge Prior to Comparate" help="Select the collection of files with the ASE Count Tables merged to Prior Calculations for the comparate [Required]"/> <param name="design" type="data" format="tabular,tsv" label="Comparate Design file" help="Enter the Comparate Design file for one condition; formatting is below [Required]"/> </inputs> <outputs> <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Generate Headers for One Comparate"> <discover_datasets pattern="(?P<name>bayesian_input_.*)" ext="tabular" directory="outputs" /> </collection> </outputs> <tests> <test> <param name="design" value="bayesian_input/comparate_df_one_condition.tsv" ftype="tsv"/> <param name="collection" value="merge_priors_testdata/bayesian_input_W55_M" ftype="tabular"/> <output_collection name="split_output" type="list"> <element name="FEATURE_ID"> <assert_contents> <has_text_matching expression="gen_headers_one_comparate"/> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ **Tool Description** The *Generate Headers for ONE Comparate* tool takes an output file created for a single user-specified comparate in the *Merge Priors to Comparate tool* and creates the headers needed for the running the Bayesian model. **NOTE:** This tool is only for user's wishing to test allelic imbalance for only one condition (ie W55_M). If testing for two or more conditions use the *Merge Two or More Comparate Datasets and Generate Headers* tool. **Required Inputs** **Collection of Merged Prior to Comparate Files [REQUIRED]** The output from the *Merge Prior to Comparate* tool is required. Example of a file containing priors merged to comparate data (W55_Mated):: FEATURE_ID prior_W55_M_both prior_W55_M_g1 prior_W55_M_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 0.802196053469128 0.114417568427753 0.0833863781031191 1 2 691 519 5020 1 29.073464805232 23.4243873865079 1075 812 7481 1 43.7266913990042 34.9168212437762 CG8920 0.866028708133971 0.0344497607655502 0.0995215311004785 1 2 29 62 647 1 10.3878993081113 9.10716914470779 38 126 920 1 15.2470189901369 12.9534815250994 CG10932 0.821591948764867 0.108417200365965 0.0699908508691674 1 2 163 122 1112 1 89.9299663299663 71.5858585858586 237 134 1881 1 144.974410774411 121.086195286195 **Comparate Design File [REQUIRED]** This tool requires a Comparate design file created by the user that contains the desired comparates. The comparates are the genomes that the user wishes to be tested as a condition to be compared in Bayesian model for allelic specific expression. **NOTE**: The Comparate Design File must be created and supplied by the user. It must explicitly list the comparate condition that the user wants to compare. The design file must contain the following columns, in order:: (1) Comparate_1: comparate 1 identifier (ex. W55_M) (2) CompID: An unique identifier that specifies the comparison (ex. W55_M) *CompID* is the same as the comparate_1 when testing allelic specific expression for only one condition An example design file: +-------------+--------+ | Comparate_1 | compID | +=============+========+ | W55_M | W55_M | +-------------+--------+ | W55_V | W55_V | +-------------+--------+ **OUTPUTS** This tool outputs one file: (1) A TSV file with the Merged Priors to Comparate output with new headers needed for Bayesian Model tool. Example of output:: +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+ | 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 | +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+ |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 | +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+ | 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 | +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+ | 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 | +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+ ]]></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>