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<tool id="metaquantome_filter" name="metaQuantome: filter" version="@VERSION@.0">
    <description>for quality, redundancy, and sample coverage</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @MAKE_SAMPS_TSV@
        metaquantome filter
        @COMMON_PARAMS@
        --expand_file '$expand_file'
        --min_peptides $min_peptides
        #if $min_pep_nsamp:
            #set $nsamp = max(int($min_peptides),int($min_pep_nsamp))
            --min_pep_nsamp $nsamp
        #else
            --min_pep_nsamp all
        #end if
        --min_children_non_leaf $min_children_non_leaf
        #if $min_child_nsamp:
            #set $nsamp = max($min_peptides,$min_child_nsamp)
            --min_child_nsamp $nsamp
        #else
            --min_child_nsamp all
        #end if
        --qthreshold $qthreshold
        --outfile='$outfile'
    ]]></command>
    <inputs>
        <expand macro="common_params"/>
        <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
                    help=""/>
        <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
            <help>
                Used for filtering to well-supported annotations. The
                number of peptides providing evidence for a term is
                the number of peptides directly annotated with that
                term plus the number of peptides annotated with any of
                its descendants. Terms with a number of peptides
                greater than or equal to min_peptides are retained.
                The default is 0.
            </help>
        </param>
        <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
            <help>
                Number of samples per group that must meet or exceed
                min_peptides. Default is 'all'.
            </help>
        </param>
        <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
            <help>
                Used for filtering to informative annotations. A term
                is retained if it has a number of children greater
                than or equal to min_children_non_leaf. The default is 0.
            </help>
        </param>
        <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
            <help>
                Number of samples per group that must meet or exceed
                min_children_nsamp. Default is 'all'.
            </help>
        </param>
        <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
            <help>
                Minimum number of intensities in each sample group.
                Any functional/taxonomic term with lower number of
                per-group intensities will be filtered out. The
                default is 3, because this is the minimum number for
                t-tests.
            </help>
        </param>

        <expand macro="output_samples_choice"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
        <expand macro="output_samples"/>
    </outputs>
    <tests>
        <test>
             <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
             <param name="mode" value="f" />
             <param name="ontology" value="go" />
             <param name="samps_src" value="build" />
             <repeat name="samps">
                 <param name="group_name" value="s1"/>
                 <param name="col_names" value="int1,int2,int3"/>
             </repeat>
             <repeat name="samps">
                 <param name="group_name" value="s2"/>
                 <param name="col_names" value="int4,int5,int6"/>
             </repeat>
             <param name="min_peptides" value="1" />
             <param name="min_pep_nsamp" value="1" />
             <param name="min_children_non_leaf" value="2" />
             <param name="min_child_nsamp" value="1" />
             <param name="qthreshold" value="2" />
             <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
metaQuantome filter
===================

The *filter* module is the second step in the metaQuantome analysis workflow. The
purpose of the filter module is to filter expanded terms to those that are
representative and well-supported by the data.


The image below illustrates the filtering process.

.. image:: filtering.png
   :width: 100 %

**Filtering methods**. The circles indicate terms, the grey arrows indicate ‘is a’ relationships, and the blue arrows indicate metaQuantome filtering procedures. (A) Filtering results by number of unique peptides. The numbers inside each term indicate the hypothetical number of peptides giving evidence to each term. (B) Filtering by the number of sample children. The number inside each term indicates the number of children (direct descendants) that term has within the sample. metaQuantome filters out terms that are neither leaves nor meet the user-specified criterion for minimum sample children (here, 2, which is the default). (C) Filtering by the number of samples in which the term was quantified.


Questions, Comments, Problems, Kudos
--------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
      ]]></help>
    <expand macro="citations" />
</tool>