view 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"

<tool id="base_reformat_design_file" name="Reformat Sample Design File"  version="21.1.13">
    <description>for use in Calculate Priors Module for BayesASE</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
  awk 'BEGIN{FS="\t"; OFS="\t"} { print $1"\t"$2"\t"$4}' ${DESIGN} | sort -u > ${OUTFILE}
]]>
    </command>
    <inputs>
        <param name="DESIGN" format="tabular,tsv" type="data" label="Input Sample Design file" help=" See help section for required format. The Sample Design file can be created using the Combine ASE Count Tables tool" />
    </inputs>
    <outputs>
        <data name="OUTFILE" format="tabular" label="${tool.name} on ${on_string}: Prior Design File"/>
    </outputs>
    <tests>
        <test>
            <param name="DESIGN" value="BASE_testdata/summarize_counts_testdata/sample_df_BASE.tabular" ftype="tabular"/>
            <output name="OUTFILE" file="BASE_testdata/summarize_counts_testdata/prior_design_file.tsv" ftype="tsv"/>
        </test>
    </tests>
    <help><![CDATA[
**Tool Description**

The Reformat Sample Design File tool takes the "Sample Design File” and modifies it to create the Priors Design File


---------------------------------------------------------------------------------------------------------------------------

**Inputs**

**Sample Design File**

The input for this tool is the Sample Design File

The Sample Design File can be created using the *Combine Counts Tables* tool.

**The Sample Design File should contain the following columns, in order:**

    (1) G1 - name of updated parental genome 1
    (2) G2 - name of updated parental genome 2
    (3) sampleID - sample identifier (no spaces in name). Consists of a combination of comparate + replicate number
    (4) comparate- contains comparate information for testing allelic imbalance

The comparate conditions must be written in the following format:

{Genotype}_{condition} (ie W1118_V)


Example of input Sample design file::

    +-------+------+---------+----------+
    |   G1  |  G2  |sampleID |comparate |
    +-------+------+---------+--------- +
    | W1118 |  W55 | W55_M_1 | W55_M    |
    +-------+------+---------+----------+
    | W1118 | W55  | W55_M_2 | W55_M    |
    +-------+------+---------+----------+
    | W1118 | W55  | W55_M_3 | W55_M    |
    +-------+------+---------+----------+
    | W1118 | W55  | W55_V_1 | W55_V    |
    +-------+------+---------+----------+


**Outputs**

(1) A Priors Design File in TSV format with the sampleID column removed and the resulting file uniqued.

Example of Priors Design File::

    +-------+------+----------+
    |   G1  |  G2  |comparate |
    +-------+------+----------+
    | W1118 |  W55 | W55_M    |
    +-------+------+----------+
    | W1118 | W55  | W55_M    |
    +-------+------+----------+
    | W1118 | W55  | W55_M    |
    +-------+------+----------+
    | W1118 | W55  | W55_V    |
    +-------+------+----------+


   ]]></help>
    <citations>
            <citation type="bibtex">@ARTICLE{Miller20BASE,
            author = {Brecca Miller, Alison Morse, Elyse Borgert, Gavin Gamble, Fei Zhou, Jeremy Newman, Fabio Marroni, Lauren M. McIntyre},
            title = {BASE: Bayesian analysis of allele specific expression reveals statistically significant regulatory variation},
            journal = {????},
            year = {in press}
            }</citation>
        </citations>
</tool>