Mercurial > repos > rjmw > dimspy_blank_filter

<tool id="dimspy_blank_filter" name="Blank Filter" version="1.0.0">
    <description> - Remove 'blank' peaks from the biological mass spectra</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        dimspy blank-filter
        --input '$hdf5_file_in'
        --output '$hdf5_file_out'
        --blank-label $blank_label
        --min-fraction $min_fraction
        --function $function
        --min-fold-change $min_fold_change
        #if $remove_blank_samples == "--remove-blank-samples"
            $remove_blank_samples
            &&
            dimspy create-sample-list
            --input '$hdf5_file_out'
            --output '$samplelist'
            --delimiter tab
        #end if
        #if $hdf5_to_txt.standard
            &&
            @HDF5_PM_TO_TXT@
        #end if
        #if $hdf5_to_txt.comprehensive
            &&
            @HDF5_PM_TO_TXT_COMPREHENSIVE@
        #end if
    ]]>
    </command>
    <inputs>
        <param name="hdf5_file_in" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" argument="--input"/>
        <param name="blank_label" type="text" value="blank" label="Label for the blank samples" argument="--blank-label">
            <validator type="empty_field"/>
        </param>
        <param name="min_fraction" type="float" min="0.0" max="1.0" value="1.0" label="Minimum fraction (percentage)" help="The percentage of samples (with a intensity value) that must beat the blank samples (peak by peak basis)" argument="--min-fraction"/>
        <param name="function" type="select" label="Function" help="Select the function that should be used to calculate the peak intensity threshold (blanks only)" argument="--function">
            <option value="mean" selected="true">mean</option>
            <option value="median">median</option>
            <option value="max">max</option>
        </param>
        <param name="min_fold_change" type="float" value="10.0" help="" argument="--min-fold-change"/>
        <param name="remove_blank_samples" type="boolean" checked="true" truevalue="--remove-blank-samples" falsevalue="" label="Remove blank samples (rows)"  help="" argument="--remove-blank-samples"/>
        <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
        <expand macro="hdf5_pm_to_txt" />
    </inputs>
    <outputs>
        <expand macro="outputs_peak_intensity_matrix" />
        <data name="samplelist" format="tsv" label="${tool.name} on ${on_string}: Sample Metadata (updated)" >
            <filter>str($remove_blank_samples) == "--remove-blank-samples"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="hdf5_file_in" value="pm_as.h5" ftype="h5"/>
            <param name="blank_label" value="blank"/>
            <param name="min_fraction" value="1.0"/>
            <param name="function" value="mean"/>
            <param name="min_fold_change" value="10.0"/>
            <param name="remove_blank_samples" value="--remove-blank-samples"/>
            <param name="delimiter" value="tab"/>
            <param name="hdf5_to_txt|standard" value="True"/>
            <param name="hdf5_to_txt|comprehensive" value="False"/>
            <param name="hdf5_to_txt|representation_samples" value="rows"/>
            <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
            <output name="hdf5_file_out" file="pm_as_bf_rmbs.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as_bf_rmbs.txt" ftype="tsv" compare="sim_size"/>
            <output name="samplelist" file="sample_list_after_bf.txt" ftype="tsv" compare="sim_size"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pm_as.h5" ftype="h5"/>
            <param name="blank_label" value="blank"/>
            <param name="min_fraction" value="1.0"/>
            <param name="function" value="mean"/>
            <param name="min_fold_change" value="10.0"/>
            <param name="remove_blank_samples" value=""/>
            <param name="delimiter" value="tab"/>
            <param name="hdf5_to_txt|standard" value="True"/>
            <param name="hdf5_to_txt|comprehensive" value="True"/>
            <param name="hdf5_to_txt|representation_samples" value="rows"/>
            <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
            <output name="hdf5_file_out" file="pm_as_bf.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as_bf.txt" ftype="tsv" compare="sim_size"/>
            <output name="matrix_comprehensive_file_out" file="peak_matrix_as_bf_compr.txt" ftype="tsv" compare="sim_size"/>
        </test>
    </tests>
    <help>
------------
Blank Filter
------------

Description
-----------

| Use this tool to remove from the user-specified peak matrix, those peaks that are present in the user-specified 'blank' class.
| A peak is subtracted from the matrix when fewer-than the 'minimum fraction' of non-blank samples have an intensity ratio (relative to the blank class) of less-than the user-specified 'min_fold_change'.
|
| In the DIMS analysis workflow, this tool is typically applied following:
| 'Process Scans' -> 'Replicate Filter' -> 'Align Samples'.
|
| The reference class defined by the user need not necessarily be a blank class and as such may be any class against which all other classes in the peak matrix are to be compared.
| For example, peaks present in a mock class 'time-point-20hr' might be subtracted from classes 'time-point-0hr' and 'time-point-4hr' if the number of samples in the 'time-point-4hr' and 'time-point-0hr' classes that have intensity ratios relative to the 'time-point-20hr' class, is fewer than the user-defined minimum fraction)

Parameters
----------

**\1. Peak Intensity Matrix (HDF5 file)** (REQUIRED)

A Peak Intensity Matrix (.h5), typically returned from the 'Align Samples' tool.

**\2. Label for the blank samples** (REQUIRED)

String indicating the name assigned to 'blank' samples in the Filelist (e.g. blank)

**\3. Minimum fraction (percentage)** (REQUIRED; default = 1)

| Numerical value ranging from 0 to 1
| Set to 0 to skip this filtering step.

**\4. ppm** (REQUIRED; default = 2.0)

| A numeric value from 0 upwards.
| Peaks with m/z differences (measured in parts-per-million) below this value are clustered together as a single feature. For clustered peaks, their intensity ratio is compared to the user-specified 'mean/median/max' intensity of any correspondingly clustered peaks from the user-specified 'blank' class.

**\5. Function** (REQUIRED; default = 'mean')

Toggle, where selection of:

- 'mean' corresponds to the use of the non-weighted average of 'blank' sample peak intensities (NA values are ignored) when calculating the 'blank' to 'non-blank' peak intensity ratio.
- 'median' corresponds to the use of the median of the 'blank' sample peak intensities (NA values are ignored) when calculating the 'blank' to 'non-blank' peak intensity ratio.
- 'max' corresponds to the use of the maximum intensity among 'blank' sample peak intensities (NA values are ignored) when calculating the 'blank' to 'non-blank' peak intensity ratio.

**\6. min_fold_change** (REQUIRED; default = 10)

Numeric value from 0 upwards. This value defines the ratio between 'non-blank' and 'blank' peak intensities, above which a peak is regarded as having been reliably detected in a sample.


**\7. Remove blank samples (rows)** (REQUIRED; default = 'YES')

Toggle, where selection of:

- 'Yes' removes samples from the output peak matrix that belong to the user-specified 'blank' class.
- 'No' retains samples from the user-specified 'blank' class in the output peak matrix.

@help_options_addtional_output@

@github_developers_contributors@

    </help>
    <expand macro="citations" />
</tool>
author	rjmw
date	Wed, 30 May 2018 09:19:03 -0400
parents	62bcdba9ddcc
children