annotate compare_flags.xml @ 2:caba07f41453 draft default tip

"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"

<tool id="secimtools_compare_flags" name="Compare Flags"  version="@WRAPPER_VERSION@">
    <description>within a flag file.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
compare_flags.py
--input $input
--output $output
--flag1 $flag1
--flag2 $flag2
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Flag File"
               help="Input tab-separated Flag File. If file is not tab separated see TIP below."/>
        <param name="flag1" type="text" size="30" optional="False" label="Column Name for Flag 1" help="Name of the column containing the first flag to compare"/>
        <param name="flag2" type="text" size="30" optional="False" label="Column Name for Flag 2" help="Name of the column containing the second flag to compare"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Flag Feature"/>
    </outputs>
    <tests>
        <test>
            <param name="input"      value="ST000006_run_order_regression_flags.tsv"/>
            <param name="flag1"      value="flag_feature_runOrder_pval_05" />
            <param name="flag2"      value="flag_feature_runOrder_pval_01" />
            <output name="output"    file="ST000006_compare_flags_output.tsv" />
        </test>
    </tests>
    <help><![CDATA[


**Tool Description**

This tool compares 2 columns containing binary indicators (flags) in a flag file and generates a 'cross tabulation' results file.
Flags from multiple flag files can by combined by first running the 'Merge_Flags' tool.

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

**Input**

The tool is intended to work with Flag Files but will work with Wide Format Datasets as well. Column names should be used instead of flag names for Wide Format Datasets.


**Flag File:**

A wide format dataset that contains flags for each sample or feature:

    +----------+---------+---------+---------+-----+
    | Feature  | flag_A  | flag_B  | flag_C  | ... |
    +==========+=========+=========+=========+=====+
    | one      | 0       | 0       | 0       | ... |
    +----------+---------+---------+---------+-----+
    | two      | 0       | 1       | 1       | ... |
    +----------+---------+---------+---------+-----+
    | three    | 0       | 1       | 0       | ... |
    +----------+---------+---------+---------+-----+
    | four     | 1       | 0       | 0       | ... |
    +----------+---------+---------+---------+-----+
    | ...      | ...     | ...     | ...     | ... |
    +----------+---------+---------+---------+-----+

**NOTE:** The 'Feature' column defines the rows within a flag file.

    @WIDE@



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

**Output**

The tool outputs a single TSV file containing the frequencies of the compared flags in the appropriate cells.
An example is shown below:

    +-----------------+----------------+-----------------+
    |                 |flag_A_[value1] | flag_A_[value2] |
    +=================+================+=================+
    | flag_B_[value1] | 12             | 22              |
    +-----------------+----------------+-----------------+
    | flag_B_[value2] | 0              | 100             |
    +-----------------+----------------+-----------------+


    ]]></help>
    <expand macro="citations"/>
</tool>