annotate add_group_rank.xml @ 2:caba07f41453 draft default tip

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

<tool id="secimtools_rank_group_wide" name="Ranked wide file"  version="@WRAPPER_VERSION@">
    <description>Generate a wide format file with ranked columns from an input wide file.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
add_group_rank.py
--wide $wide
--design $design
--out $out
#if $ngroup:
    --ngroup $ngroup
#end if
--uniqID $uniqID
    ]]></command>
    <inputs>
        <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
        <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/>
    </inputs>
    <outputs>
        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/>
    </outputs>
    <tests>
      <test>
	<param name="wide" value="ST000006_data.tsv"/>
	<param name="design" value="ST000006_design.tsv"/>
	<param name="uniqID" value="Retention_Index" />
	<param name="ngroup" value="100" />
	<output name="out" file="ST000006_add_group_rank_output_wide.tsv" />
      </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool is used to generate a wide format file with each column being ranked in the input wide format dataset.

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

**Input**

    - Two input datasets are required.
    
    An example of input wide file is like:

        +---------+---------+---------+---------+-----+
        | Feature | sample1 | sample2 | sample3 | ... |
        +=========+=========+=========+=========+=====+
        | one     | 10.2    | 20      | 10      | ... |
        +---------+---------+---------+---------+-----+
        | two     | 5.1     | 22      | 30      | ... |
        +---------+---------+---------+---------+-----+
        | three   | 30.5    | 27      | 2       | ... |
        +---------+---------+---------+---------+-----+
        | four    | 32.9    | 17      | 8       | ... |
        +---------+---------+---------+---------+-----+
        | ...     | ...     | ...     | ...     | ... |
        +---------+---------+---------+---------+-----+

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

**Output**

The user will get a output file from the tool:

- a wide format file with each column being ranked.

The output wide file for the example above will be like:
        
+---------+---------+---------+---------+-----+
| Feature | sample1 | sample2 | sample3 | ... |
+=========+=========+=========+=========+=====+
| one     | 2       | 2       | 3       | ... |
+---------+---------+---------+---------+-----+
| two     | 1       | 3       | 4       | ... |
+---------+---------+---------+---------+-----+
| three   | 3       | 4       | 1       | ... |
+---------+---------+---------+---------+-----+
| four    | 4       | 1       | 2       | ... |
+---------+---------+---------+---------+-----+
| ...     | ...     | ...     | ...     | ... |
+---------+---------+---------+---------+-----+

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