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comparison merge_comparates_and_gen_headers_for_bayesian.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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1 <tool id="merge_comparates_and_gen_headers_for_bayesian" name="Merge Comparate Datasets and Generate Headers" version="21.1.13"> | |
2 <description>for Bayesian Analysis of Allelic Imbalance</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command><![CDATA[ | |
8 mkdir outputs; | |
9 cd outputs; | |
10 merge_comparates_generate_bayesian_headers.py | |
11 --output=`pwd` | |
12 --collection_identifiers="${','.join($collection.keys())}" | |
13 --collection_filenames="${','.join(map(str, $collection))}" | |
14 --design=$design | |
15 ]]></command> | |
16 <inputs> | |
17 <param name="collection" type="data_collection" collection_type="list" label="Collection of Comparate Datasets containing Prior Probability Estimates" help="Select the collection containing files to be merged. [Required]"/> | |
18 <param name="design" type="data" format="tabular,tsv" label=" Comparate Design file" help="Select your Comparate Design file. See below for correct formatting of this design file [Required]"/> | |
19 </inputs> | |
20 <outputs> | |
21 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Merged Comparates with Headers"> | |
22 <discover_datasets pattern="(?P<name>bayesian_input_.*)" ext="tabular" sort_by="reverse_filename" directory="outputs" /> | |
23 </collection> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="design" value="bayesian_input/comparate_design_file.tsv" ftype="tsv"/> | |
28 <param name="collection" value="merge_priors_testdata/merge_priors_to_comparate" ftype="data_collection"/> | |
29 <output_collection name="split_output" type="list"> | |
30 <element name="FEATURE_ID"> | |
31 <assert_contents> | |
32 <has_text_matching expression="Merge_comparates_and_gen_headers"/> | |
33 </assert_contents> | |
34 </element> | |
35 </output_collection> | |
36 </test> | |
37 </tests> | |
38 <help><![CDATA[ | |
39 **Tool Description** | |
40 | |
41 The Merge Comparates and Generate Headers tool merges the comparate datasets containing the priors (generated by the Merge Priors tool) as specified in the Comparate Design File. | |
42 New headers are created by mapping the user-specified comparate names to a general variable. | |
43 | |
44 **Inputs** | |
45 | |
46 **Collection of Merged Prior to Comparate Files [REQUIRED]** | |
47 | |
48 The collection of datasets containing summarized ASE Count Tables with Prior Estimates generated by the Merge Priors to Comparate tool. | |
49 | |
50 Example of a merged prior to comparate file in the collection (W55_Mated):: | |
51 | |
52 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 | |
53 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 | |
54 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 | |
55 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 | |
56 | |
57 | |
58 | |
59 **Comparate Design File [REQUIRED]** | |
60 | |
61 This tool requires a Comparate Design File created by the user that contains the desired comparates to be tested. | |
62 | |
63 **NOTE**:The Comparate Design File is created and supplied by the user. It explicitly lists the comparates that the user wants to compare. | |
64 | |
65 The Comparate Design File must contain the following columns, in order:: | |
66 | |
67 (1) Comparate_1: comparate 1 identifier (ex. W55_M) | |
68 (2) Comparate_2: comparate 2 identifier (ex. W55_V) | |
69 (3) CompID: An unique identifier that specifies the comparison (ex. W55_M_V) | |
70 | |
71 An example design file: | |
72 | |
73 +-------------+-------------+--------+ | |
74 | Comparate_1 | Comparate_2 | compID | | |
75 +=============+=============+========+ | |
76 | W55_M | W55_V | W55_M_V| | |
77 +-------------+-------------+--------+ | |
78 | |
79 **Outputs** | |
80 | |
81 -This tool outputs the following: | |
82 | |
83 A TSV file containing all comparates as defined in the Comparate Design File. | |
84 | |
85 In the example below, the W55 Virgin and W55 Mated comparates are in a single file where c1=W55_Virgin and c2=W55_Mated. | |
86 | |
87 Example of Output:: | |
88 | |
89 +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ | |
90 | 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 | | |
91 +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ | |
92 |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 | | |
93 +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ | |
94 | 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 | | |
95 +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ | |
96 | 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 | | |
97 +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+ | |
98 | |
99 | |
100 ]]></help> | |
101 <citations> | |
102 <citation type="bibtex">@ARTICLE{Miller20BASE, | |
103 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}, | |
104 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, | |
105 journal = {????}, | |
106 year = {submitted for publication} | |
107 }</citation> | |
108 </citations> | |
109 </tool> |