Mercurial > repos > malex > bayesase
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_comparate_design_file.xml Thu Jan 14 21:51:36 2021 +0000 @@ -0,0 +1,65 @@ +<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>