Mercurial > repos > malex > bayesase
view 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 |
---|---|
date | Thu, 14 Jan 2021 21:51:36 +0000 |
parents | |
children |
line wrap: on
line source
<tool id="base_check_comparate_design_file" name="Check Comparate Design File" version="21.1.13"> <description>for correct formatting and header names </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command><![CDATA[ check_comparate_design_file.py --design=$design --compNum=$compNum --out=$out ]]></command> <inputs> <param name="design" type="data" format="tabular,tsv" label="Select Comparate Design File" help="Design file containing comparates and conditions. Please refer to the BASE User Guide for help."/> <param name="compNum" size="30" type="select" value="" display="radio" label="Comparate Number" help="Select the number of comparate conditions for the data."> <option value="1">One Comparate</option> <option value="2">Two Comparates</option> </param> </inputs> <outputs> <data format="tabular" name="out" label="${tool.name} on ${on_string}: Comparate Design criteria"/> </outputs> <tests> <test> <param name="design" ftype="data" value="check_comparate_design_file/df_comparate.tsv"/> <param name="compNum" ftype="text" value="1"/> <output name="out" /> </test> </tests> <help><![CDATA[ **Tool Description** 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. **The design file should contain the following columns, in order:** (5) Comparate_1: first comparate. For example, 'W55_M' which is a combination of genotype W55 and condition mated. (6) Comparate_2: second comparate. For example 'W55_V' which is a combination of genotype W55 and condition virgin (7) CompID: A unique identifier that describes the comparison. For example, 'W55_M_V', for the comparison of W55 mated to W55 virgin. An example design file for two comparates:: Comparate_1 Comparate_2 compID W55_M W55_V W55_M_V **Outputs** (1) a logfile with information about whether the column names are correct (2) a text file containing a list of any missing or misspelled labels, if present ]]></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>