annotate blank_feature_filtering_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_blank_feature_filtering_flags" name="Blank Feature Filtering (BFF)" version="@WRAPPER_VERSION@">
    <description> - Calculate LOD and flag features in non-blank samples below threshold.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
blank_feature_filtering_flags.py
--input $input
--design $design
--uniqID $uniqID
--group $group
--blank "$blank"
--bff $bff
--criteria $cv
--outflags $outflags
--outbff $outbff
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input tab-separated wide format dataset. If not tab separated see TIP below."/>
    <param name="design" type="data" format="tabular" label="Design File" help="Design file, tab separated. Note: you need a 'sampleID' column. If not tab-separated, see TIP below."/>
    <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
    <param name="group" type="text" size="30" value="" optional="true" label="Group/Treatment" help="Name of the column in your design file that contains classification information."/>
    <param name="blank" type="text" size="30" optional="true" label="Blank Name" help="Name given to the blank samples in your Group/Treatment column. Used to calculate baseline in filtering."/>
    <param name="bff" type="integer" size="30" value="5000" optional="true" label="BFF Threshold" help="Default value to use as the limit of detection."/>
    <param name="cv" type="integer" size="30" value="100" optional="true" label="Criterion Value" help="Number of times the signal in the samples shoud be stronger than the corresponding signal in the blanks."/>
    </inputs>
    <outputs>
        <data format="tabular" name="outflags" label="${tool.name} on ${on_string}: Flags"/>
    <data format="tabular" name="outbff" label="${tool.name} on ${on_string}: Value"/>
    </outputs>
    <tests>
        <test>
            <param name="input"  value="TEST0000_data.tsv"/>
            <param name="design" value="TEST0000_design.tsv"/>
            <param name="uniqID" value="rowID" />
            <param name="group"  value="group_combined" />
            <param name="blank"  value="blank" />
            <param name="bff"    value="5000" />
            <param name="cv"     value="100" />
            <output name="outflags" file="TEST0000_blank_feature_filtering_flags_outflags.tsv" />
            <output name="outbff"   file="TEST0000_blank_feature_filtering_flags_outbff.tsv" />
        </test>
    </tests>
<help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

**NOTE:** The tool is relevant for Liquid Chromatography Mass Spectroscopy (LC-MS) data analysis and removes “noise” from the data using values of features in the blank samples as a reference.
The tool becomes relevant when the values of features in the experimental samples are not much larger than the values of the same features in the blank samples.
The features with such a signal are treated as noise inherited by the sample due to the instrument and are flagged by the tool.

The computed BFF Threshold for each feature is equal to ((3*Standard Deviation of the blank group) + (the average of the blank group)) and is calculated aross blank samples only.
If, for a given feature, the computed BFF Threshold is less than or equal to 0, the user specified BFF Threshold overrides the computed BFF Threshold (default value for user specfied BFF Threshold is 5000).

The user specified BFF Threshold becomes relevant when the blank group contains a lot of zero values or is on log-transformed scale.

A feature is flagged as below the detection limit for a given group if the ratio ((group mean – BFF Threshold) / BFF Threshold) is less than the Criterion Value (default 100) for the average within the group.

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

**Input**

    - Two input datasets are required.

@WIDE@

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

@METADATA@

@UNIQID@

@GROUP@

**Blank Name**

    - Name given to the blanks samples in your Group/Treatment column. Used to calculate the computed BFF Threshold for filtering.

**BFF Threshold**

    - User-specified BFF threshold to use as the limit of detection. The default value is 5000.

**Criterion Value**

    - Number of times the signal in the experimental samples should be greater than the corresponding signal in the blanks. 

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

**Output**

This tool outputs two files:

(1) a TSV file with values that were compared to the Criterion Value and
(2) a TSV file containing flags for each feature.  Flag values of one (1) correspond to features which failed to satisfy the BFF Threshold Criterion Value and are considered below the detection limit for the given group.


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