annotate summary.xml @ 0:ceb70f0dd898 draft default tip

"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"

<tool id="csvtk_summary" name="csvtk-summary" version="@VERSION@+@GALAXY_VERSION@">
    <description> statistics of selected fields</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

## Set Up Input ##
##################

#set input_list = list()
#for $repeat in $field
    #silent $input_list.append(str($repeat.column_text.in_text) + ":" + str($repeat.analysis_type))
#end for

#set input_total = ",".join($input_list)

###################
## Start Command ##
###################

csvtk summary --num-cpus "\${GALAXY_SLOTS:-1}"

    ## Add additional flags as specified ##
    #######################################
    $global_param.illegal_rows
    $global_param.empty_rows
    $global_param.header
    $global_param.lazy_quotes

    ## Set Tabular input/output flag if input is tabular ##
    #######################################################
    #if $in_1.is_of_type("tabular"):
        -t -T
    #end if

    ## Set Input ##
    ###############
    '$in_1'

    ## Specify fields ##
    ####################
    -f '$input_total'

    ## other ##
    ###########

    #if $group_field.select_group != "none"
        -g '$group_field.in_text'
    #end if

    -s '$extra.separator'
    -S '$extra.rand_int'
    -n '$decimal_width'
    $ignore_non_digits
    

    ## To output ##
    ###############
    > summary

    ]]></command>
    <inputs>
        <expand macro="singular_input" />
        <repeat name="field" title="Select Column and Operator" min="1">
            <expand macro="singular_fields_input" />
            <param name="analysis_type" type="select" label="Analysis Type" help="Select analysis type to do on the chosen field">
                <option value="collapse">Collapse</option>
                <option value="count">Count</option>
                <option value="countn">Count of Digits (countn)</option>
                <option value="countunique">Count Unique</option>
                <option value="first">First Value</option>
                <option value="last">Last Value</option>
                <option value="max">Maximum</option>
                <option value="mean">Mean</option>
                <option value="median">Median</option>
                <option value="min">Minimum</option>
                <option value="prod">Product of the Elements</option>
                <option value="q1">q1</option>
                <option value="q2">q2</option>
                <option value="q3">q3</option>
                <option value="rand">Random Value</option>
                <option value="entropy">Shannon Entropy</option>
                <option value="stdev">Standard Deviation</option>
                <option value="sum">Sum</option>
                <option value="uniq">Unique</option>
                <option value="variance">Variance</option>
            </param>
        </repeat>
        <expand macro="groups_input" />
        <param name="decimal_width" type="integer" value="2" argument="-n"
            label="Number of Decimals"
            help="Limit float to N decimal places"
        />
        <param name="ignore_non_digits" type="boolean" checked="false" argument="-i"
            truevalue="-i"
            falsevalue=""
            label="Ignore non-digits"
            help="Ignore non-digit values in columns. Ex. NA or N/A"
        />
        <section name="extra" title="Specific Optional Analysis Modifiers" expanded="false">
            <param name="separator" type="text" value="; " argument="-s"
                label="Collapse Separator String"
                help="Input string of characters that will separate collapsed columns. The ' character is not allowed">
                <expand macro="text_sanitizer" />
            </param>
            <param name="rand_int" type="integer" value="11" argument="-S"
                label="Random Value Seed"
                help="specify an integer"
            />
        </section>
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" name="summary" from_work_dir="summary" label="${in_1.name} summary of analyses" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="plot.csv" />
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="collapse" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="count" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="countn" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="countunique" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="entropy" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="first" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="last" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="max" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="mean" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="median" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="min" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="prod" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="q1" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="q2" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="q3" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="rand" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="stdev" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="sum" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="analysis_type" value="uniq" />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <param name="analysis_type" value="variance" />
            </repeat>
            <conditional name="group_field">
                <param name="select_group" value="string" />
                <param name="in_text" value="1" />
            </conditional>
            <output name="summary" >
                <assert_contents>
                    <has_text text="collapse" />
                    <has_text text="count" />
                    <has_text text="countn" />
                    <has_text text="countunique" />
                    <has_text text="entropy" />
                    <has_text text="first" />
                    <has_text text="last" />
                    <has_text text="max" />
                    <has_text text="mean" />
                    <has_text text="median" />
                    <has_text text="min" />
                    <has_text text="prod" />
                    <has_text text="q1" />
                    <has_text text="q2" />
                    <has_text text="q3" />
                    <has_text text="rand" />
                    <has_text text="stdev" />
                    <has_text text="sum" />
                    <has_text text="uniq" />
                    <has_text text="variance" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Summary Help
--------------------

Info
####

Csvtk Summary works to allow the use of a variety of analysis tools on the selected columns(s) and display one output at the end 

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


Usage
#####

To run csvtk-summary, all you need is a valid (as defined above) CSV or TSV file with any column(s) that you want to
run one of the analyses on.

Analyses include:

- Collapse

- Count

- Count Numbers (countn)

- Count Unique

- First Value Selection

- Last Value Selection

- Maximum

- Mean

- Median

- Minimum

- q1

- q2

- q3

- Random Value Selection

- Shannon Entropy

- Sum

- Unique Values

- Variance

More information on these can be found on the `csvtk website. <https://bioinf.shenwei.me/csvtk/usage/#summary>`_

**Example Summary Input**

Input table:

+-------+--------+
| Group | Length |
+=======+========+
| A     | 1500   |
+-------+--------+
| B     | 1000   |
+-------+--------+
| B     | 1500   |
+-------+--------+
| B     | 2000   |
+-------+--------+

Suppose you wanted to group the values based on column 1 of the input table and then find out the mean lenght and maximum length for each group.
You would input this into csvtk-summary by creating 2 input repeats where the first one selects "column 2" and an analysis of "mean" and the
second one selects "column 2" with an analysis of "maximum".

Running this would generate the following output:

+-------+-------------+------------+
| Group | Length:mean | Length:max |
+=======+=============+============+
| A     | 1500        | 1500       |
+-------+-------------+------------+
| B     | 1500        | 2000       |
+-------+-------------+------------+

--------


@HELP_COLUMNS@


@HELP_END_STATEMENT@


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