annotate remove_user_specified_row_col.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

<tool id="secimtools_remove_user_specified_features" name="Remove User-Specified Features or Samples" version="@WRAPPER_VERSION@">
    <description>from the data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
remove_user_specified_row_col.py
--input $input
--design $design
--ID $uniqID
--outWide $outWide
--row $rowID
--col $colID
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset"
               help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File"
               help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID"
               help="Name of the column in your wide dataset that has unique identifiers."/>
        <param name="rowID" type="text" size="30" value="" label="Features to drop [Optional]."
               help="Space-separated list of unique identifiers (rows) in your wide dataset to delete."/>
        <param name="colID" type="text" size="30" value="" label="Samples to drop [Optional]."
               help="Space-separated list of unique sampleIDs (columns) to be removed from the wide dataset."/>
    </inputs>
    <outputs>
        <data format="tabular" name="outWide" label="${tool.name} on ${on_string}: Dropped wide"/>
    </outputs>
    <tests>
        <test>
            <param name="input"       value="fly_test_sbys.tsv"/>
            <param name="design"      value="fly_test_design.tsv"/>
            <param name="uniqID"      value="rowID" />
            <param name="rowID"       value="_15" />
            <param name="colID"       value="r101_V_3" />
            <output name="outWide"    file="fly_remove_specified_features_samples_wide.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool removes user-specified features (rows) or samples (columns) from a wide format dataset.
The user manually enters space delimited rows (features) and / or columns (samples).

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

**Input**

    - Two input datasets are required.

@WIDE@

**NOTE:** The sample IDs must match the sample IDs in the Design File
(below). Extra columns will automatically be ignored.

@METADATA@

@UNIQID@

**Unique ID for Flag file (feature ID or sample ID).**

    - Name of the column in your Wide dataset that contains unique Feature IDs.

**rowID.** 

    - Name of the row(s) in your Wide dataset to drop.

**colID.**

    - Name of the column(s) in your Wide dataset to drop.

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

**Output**

This tool outputs one TSV file:

(1) A wide format dataset generated from the input wide format dataset where features and/or samples specified by the user have been removed.

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