Mercurial > repos > malex > bayesase
comparison check_comparate_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 |
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date | Thu, 14 Jan 2021 21:51:36 +0000 |
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1 <tool id="base_check_comparate_design_file" name="Check Comparate Design File" version="21.1.13"> | |
2 <description>for correct formatting and header names </description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command><![CDATA[ | |
8 check_comparate_design_file.py | |
9 --design=$design | |
10 --compNum=$compNum | |
11 --out=$out | |
12 ]]></command> | |
13 <inputs> | |
14 <param name="design" type="data" format="tabular,tsv" label="Select Comparate Design File" help="Design file containing comparates and conditions. Please refer to the BASE User Guide for help."/> | |
15 <param name="compNum" size="30" type="select" value="" display="radio" label="Comparate Number" help="Select the number of comparate conditions for the data."> | |
16 <option value="1">One Comparate</option> | |
17 <option value="2">Two Comparates</option> | |
18 </param> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Comparate Design criteria"/> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="design" ftype="data" value="check_comparate_design_file/df_comparate.tsv"/> | |
26 <param name="compNum" ftype="text" value="1"/> | |
27 <output name="out" /> | |
28 </test> | |
29 </tests> | |
30 <help><![CDATA[ | |
31 **Tool Description** | |
32 | |
33 This tool checks to make sure the design file is formatted correctly and has all needed headers. It also verifies that there are no missing labels. | |
34 | |
35 **The design file should contain the following columns, in order:** | |
36 | |
37 | |
38 (5) Comparate_1: first comparate. For example, 'W55_M' which is a combination of genotype W55 and condition mated. | |
39 (6) Comparate_2: second comparate. For example 'W55_V' which is a combination of genotype W55 and condition virgin | |
40 (7) CompID: A unique identifier that describes the comparison. For example, 'W55_M_V', for the comparison of W55 mated to W55 virgin. | |
41 | |
42 | |
43 | |
44 An example design file for two comparates:: | |
45 | |
46 Comparate_1 Comparate_2 compID | |
47 W55_M W55_V W55_M_V | |
48 | |
49 | |
50 **Outputs** | |
51 | |
52 (1) a logfile with information about whether the column names are correct | |
53 (2) a text file containing a list of any missing or misspelled labels, if present | |
54 | |
55 ]]></help> | |
56 <citations> | |
57 <citation type="bibtex">@ARTICLE{Miller20BASE, | |
58 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}, | |
59 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, | |
60 journal = {????}, | |
61 year = {submitted for publication} | |
62 } | |
63 </citation> | |
64 </citations> | |
65 </tool> |