Mercurial > repos > malex > bayesase
comparison reformat_sample_design_file.xml @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
author | malex |
---|---|
date | Thu, 14 Jan 2021 21:51:36 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:e979cb57a5d5 |
---|---|
1 <tool id="base_reformat_design_file" name="Reformat Sample Design File" version="21.1.13"> | |
2 <description>for use in Calculate Priors Module for BayesASE</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command> | |
8 <![CDATA[ | |
9 awk 'BEGIN{FS="\t"; OFS="\t"} { print $1"\t"$2"\t"$4}' ${DESIGN} | sort -u > ${OUTFILE} | |
10 ]]> | |
11 </command> | |
12 <inputs> | |
13 <param name="DESIGN" format="tabular,tsv" type="data" label="Input Sample Design file" help=" See help section for required format. The Sample Design file can be created using the Combine ASE Count Tables tool" /> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="OUTFILE" format="tabular" label="${tool.name} on ${on_string}: Prior Design File"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="DESIGN" value="BASE_testdata/summarize_counts_testdata/sample_df_BASE.tabular" ftype="tabular"/> | |
21 <output name="OUTFILE" file="BASE_testdata/summarize_counts_testdata/prior_design_file.tsv" ftype="tsv"/> | |
22 </test> | |
23 </tests> | |
24 <help><![CDATA[ | |
25 **Tool Description** | |
26 | |
27 The Reformat Sample Design File tool takes the "Sample Design File” and modifies it to create the Priors Design File | |
28 | |
29 | |
30 --------------------------------------------------------------------------------------------------------------------------- | |
31 | |
32 **Inputs** | |
33 | |
34 **Sample Design File** | |
35 | |
36 The input for this tool is the Sample Design File | |
37 | |
38 The Sample Design File can be created using the *Combine Counts Tables* tool. | |
39 | |
40 **The Sample Design File should contain the following columns, in order:** | |
41 | |
42 (1) G1 - name of updated parental genome 1 | |
43 (2) G2 - name of updated parental genome 2 | |
44 (3) sampleID - sample identifier (no spaces in name). Consists of a combination of comparate + replicate number | |
45 (4) comparate- contains comparate information for testing allelic imbalance | |
46 | |
47 The comparate conditions must be written in the following format: | |
48 | |
49 {Genotype}_{condition} (ie W1118_V) | |
50 | |
51 | |
52 Example of input Sample design file:: | |
53 | |
54 +-------+------+---------+----------+ | |
55 | G1 | G2 |sampleID |comparate | | |
56 +-------+------+---------+--------- + | |
57 | W1118 | W55 | W55_M_1 | W55_M | | |
58 +-------+------+---------+----------+ | |
59 | W1118 | W55 | W55_M_2 | W55_M | | |
60 +-------+------+---------+----------+ | |
61 | W1118 | W55 | W55_M_3 | W55_M | | |
62 +-------+------+---------+----------+ | |
63 | W1118 | W55 | W55_V_1 | W55_V | | |
64 +-------+------+---------+----------+ | |
65 | |
66 | |
67 **Outputs** | |
68 | |
69 (1) A Priors Design File in TSV format with the sampleID column removed and the resulting file uniqued. | |
70 | |
71 Example of Priors Design File:: | |
72 | |
73 +-------+------+----------+ | |
74 | G1 | G2 |comparate | | |
75 +-------+------+----------+ | |
76 | W1118 | W55 | W55_M | | |
77 +-------+------+----------+ | |
78 | W1118 | W55 | W55_M | | |
79 +-------+------+----------+ | |
80 | W1118 | W55 | W55_M | | |
81 +-------+------+----------+ | |
82 | W1118 | W55 | W55_V | | |
83 +-------+------+----------+ | |
84 | |
85 | |
86 ]]></help> | |
87 <citations> | |
88 <citation type="bibtex">@ARTICLE{Miller20BASE, | |
89 author = {Brecca Miller, Alison Morse, Elyse Borgert, Gavin Gamble, Fei Zhou, Jeremy Newman, Fabio Marroni, Lauren M. McIntyre}, | |
90 title = {BASE: Bayesian analysis of allele specific expression reveals statistically significant regulatory variation}, | |
91 journal = {????}, | |
92 year = {in press} | |
93 }</citation> | |
94 </citations> | |
95 </tool> |