annotate 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"

<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>