annotate datamash-ops.xml @ 2:562f3c677828 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7

<?xml version="1.0"?>
<tool id="datamash_ops" name="Datamash" version="@WRAPPER_VERSION@">
    <description>(operations on tabular data)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        <![CDATA[
            datamash
                $header_in
                $header_out
                $need_sort
                $print_full_line
                $ignore_case
                #if str($grouping).strip()
                --group '$grouping'
                #end if
                #for $oper in $operations
                    ${oper.op_name}
                    ${oper.op_column}
                #end for
                < $in_file > '$out_file'
          ]]>
    </command>
    <expand macro="inputs_outputs">
        <param help="Example: to group by the first and fourth fields, use 1,4." label="Group by fields" name="grouping" type="text">
            <validator message="Invalid value in field. Allowed values are 0-9, space, comma." type="regex">^[0-9, ]*$</validator>
        </param>
        <param falsevalue="" help="--header-in" label="Input file has a header line" name="header_in" truevalue="--header-in" type="boolean" />
        <param falsevalue="" help="--header-out" label="Print header line" name="header_out" truevalue="--header-out" type="boolean" />
        <param falsevalue="" help="--sort" label="Sort input" name="need_sort" truevalue="--sort" type="boolean" />
        <param falsevalue="" help="--full" label="Print all fields from input file" name="print_full_line" truevalue="--full" type="boolean" />
        <param falsevalue="" help="--ignore-case" label="Ignore case when grouping" name="ignore_case" truevalue="--ignore-case" type="boolean" />
        <repeat default="1" min="1" name="operations" title="Operation to perform on each group">
            <param name="op_name" type="select" label="Type">
                <option value="count">count</option>
                <option value="sum">sum</option>
                <option value="min">minimum</option>
                <option value="max">maximum</option>
                <option value="absmin">Absolute minimum</option>
                <option value="absmax">Absolute maximum</option>
                <option value="mean">Mean</option>
                <option value="pstdev">Population Standard deviantion</option>
                <option value="sstdev">Sample Standard deviantion</option>
                <option value="median">Median</option>
                <option value="q1">1st quartile</option>
                <option value="q3">3rd quartile</option>
                <option value="iqr">Inter-quartile range</option>
                <option value="mad">Median Absolute Deviation</option>
                <option value="pvar">Variance (population)</option>
                <option value="svar">Variance (sample)</option>
                <option value="sskew">Skewness (sample)</option>
                <option value="pskew">Skewness (population)</option>
                <option value="skurt">Kurtosis (sample)</option>
                <option value="pkurt">Kurtosis (population)</option>
                <option value="jarque">Jarque-Bera Normality test</option>
                <option value="dpo">D Agostino-Pearson Omnibus Normality Test</option>
                <option value="mode">Mode</option>
                <option value="antimode">Anti-Mode</option>
                <option value="rand">One random value from the group</option>
                <option value="unique">Combine all unique values</option>
                <option value="collapse">Combine all values</option>
                <option value="countunique">Count Unique values</option>
            </param>
            <param name="op_column" data_ref="in_file" label="On column" type="data_column" />
        </repeat>
    </expand>
    <tests>
        <test>
            <param name="in_file" value="group_compute_input.txt" ftype="tabular" />
            <param name="grouping" value="2" />
            <param name="header_in" value="true" />
            <param name="header_out" value="true" />
            <param name="need_sort" value="true" />
            <param name="print_full_line" value="false" />
            <param name="ignore_case" value="false" />
            <repeat name="operations">
                <param name="op_name" value="sum" />
                <param name="op_column" value="3" />
            </repeat>
            <output file="group_compute_output.txt" name="out_file" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
@HELP_HEADER@

**Syntax**

This tools performs common operations (such as summing, counting, mean, standard-deviation) on input file, based on tabular data. The tool can also optionaly group the input based on a given field.

-----

**Example 1**

- Find the average score in statistics course of college students, grouped by their college major. The input file has three fields (Name,Major,Score) and a header line::

    Name        Major            Score
    Bryan       Arts             68
    Isaiah      Arts             80
    Gabriel     Health-Medicine  100
    Tysza       Business         92
    Zackery     Engineering      54
    ...
    ...

- Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::

    GroupBy(Major)     mean(Score)   sstdev(Score)
    Arts               68.9474       10.4215
    Business           87.3636       5.18214
    Engineering        66.5385       19.8814
    Health-Medicine    90.6154       9.22441
    Life-Sciences      55.3333       20.606
    Social-Sciences    60.2667       17.2273

This sample file is available at http://www.gnu.org/software/datamash .

**Example 2**

- Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz

- List the number and identifiers of isoforms per gene. The gene identifier is in column 13, the isoform/transcript identifier is in column 2. Grouping by column 13 and performing **count** and **Combine all values** on column 2, gives::

    GroupBy(field-13)     count(field-2)     collapse(field-2)
    A1BG                  1                  NM_130786
    A1BG-AS1              1                  NR_015380
    A1CF                  6                  NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
    A2M                   1                  NM_000014
    A2M-AS1               1                  NR_026971
    A2ML1                 2                  NM_001282424,NM_144670
    ...

- Count how many transcripts are listed for each chromosome and strand. Chromosome is on column 3, Strand is in column 4. Transcript identifiers are in column 2. Grouping by columns **3,4** and performing operation **count** on column 2, gives::

    GroupBy(field-3)     GroupBy(field-4)     count(field-2)
    chr1                 +                    2456
    chr1                 -                    2431
    chr2                 +                    1599
    chr2                 -                    1419
    chr3                 +                    1287
    chr3                 -                    1249
    ...

@HELP_FOOTER@
]]>
    </help>
</tool>