annotate macros.xml @ 0:a288e0146c2e draft default tip

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

<macros>
    <token name="@VERSION@">0.20.0</token>
    <token name="@GALAXY_VERSION@">galaxy0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">csvtk</requirement>
        </requirements>
    </xml>
    <xml name="version_cmd">
        <version_command>csvtk version</version_command>
    </xml>
    <xml name="text_sanitizer">
        <sanitizer>
            <valid initial="string.printable">
                    <remove value="&apos;"/>
            </valid>
        </sanitizer>
    </xml>
    <xml name="multi_input">
        <param type="data" name="in_1" format="csv,tabular"
            multiple="true" optional="false"
            label="Specify TSV or CSV file inputs"
            help="Input tsv or csv files to analyze. HOWEVER, they must all be the **same file type** or the tool will fail/not give correct results!"
        />
    </xml>
    <xml name="singular_input">
        <param type="data" name="in_1" format="csv,tabular"
            multiple="false" optional="false"
            label="Specify an input TSV or CSV file"
            help="Input a TSV or CSV file to work on"
        />
    </xml>
    <xml name="ignore_case">
        <param type="boolean" name="ignore_case"
            falsevalue="" truevalue="-i"
            checked="false"
            argument="-i"
            label="Ignore cell case?"
            help="ABC == abc"
        />
    </xml>
    <xml name="global_parameters">
        <section name="global_param" title="csvtk Global Parameters" expanded="false">
            <param type="boolean" name="header"
                falsevalue="-H" truevalue=""
                checked="true"
                argument="-H"
                label="Input file has a header line"
            />
            <param type="boolean" name="illegal_rows"
                falsevalue="" truevalue="-I"
                checked="false"
                argument="-I"
                label="Ignore illegal rows"
                help="Use if file has illegal rows as defined in the help section"
            />
            <param type="boolean" name="empty_rows"
                falsevalue="" truevalue="-E"
                checked="false"
                argument="-E"
                label="Ignore empty rows"
                help="Ignore rows with no data (only needed if input has empty rows)"
            />
            <param type="boolean" name="lazy_quotes"
                falsevalue="" truevalue="-l"
                checked="false"
                argument="-l"
                label="File has Lazy quotes"
                help="(TSV files only) If Yes, a quote may appear in an unquoted field and a non-doubled quote may appear in a quoted field"
            />
        </section>
    </xml>
    <xml name="fields_input">
        <conditional name="column_text" >
            <param type="select" name="select" label="Select input column(s) based on" argument="-F -f">
                <option value="string">Column Name(s)</option>
                <option value="column">Column Number(s)</option>
            </param>
            <when value="column">
                <param type="data_column" name="in_text"
                    data_ref="in_1"
                    multiple="true"
                    label="Input column number(s)"
                    help="Select column(s) to use for analysis"
                />
            </when>
            <when value="string">
                <param type="text" name="in_text"
                    optional="false"
                    label="Input column name(s)"
                    help="Multiple columns can be given if separated by a ' , '. 
                    Column numbers can be given too - ex. '1,2' will target columns 1 and 2. 
                    Please see the help section below for more detailed info">
                    <sanitizer>
                        <valid initial="string.printable">
                                <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="singular_fields_input">
        <conditional name="column_text" >
            <param type="select" name="select" label="Select input column based on" argument="-f">
                <option value="string">Column Name</option>
                <option value="column">Column Number</option>
            </param>
            <when value="column">
                <param type="data_column" name="in_text"
                    data_ref="in_1"
                    multiple="false"
                    label="Input column number"
                    help="Select column to use for analysis"
                />
            </when>
            <when value="string">
                <param type="text" name="in_text"
                    optional="false"
                    label="Input column name"
                    help="Input column name or number ex. 'Length' or '1'.  
                    Please see the help section below for more detailed info">
                    <sanitizer>
                        <valid initial="string.printable">
                                <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="plot_field">
        <conditional name="column_text" >
            <param type="select" name="select" label="Select input data column based on" argument="-f">
                <option value="string">Column Name</option>
                <option value="column">Column Number</option>
            </param>
            <when value="column">
                <param type="data_column" name="in_text"
                    data_ref="in_1"
                    multiple="false"
                    label="Input data column number"
                />
            </when>
            <when value="string">
                <param type="text" name="in_text"
                    optional="false"
                    label="Input data column name"
                    help="Can use column name or column number">
                    <sanitizer>
                        <valid initial="string.printable">
                                <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="groups_input">
        <conditional name="group_field" >
            <param type="select" name="select_group" label="Select column to group data" argument="-g" optional="false" help="Specify a single column that is used to create data groups. An example is shown in the help section">
                <option value="none">None</option>
                <option value="string">Column Name</option>
                <option value="column">Column Number</option>
            </param>
            <when value="none" />
            <when value="column">
                <param type="data_column" name="in_text"
                    data_ref="in_1"
                    multiple="false"
                    label="Group by column number"
                />
            </when>
            <when value="string">
                <param type="text" name="in_text"
                    optional="false"
                    label="Group by column name"
                    help="Can use column name or number">
                    <sanitizer>
                        <valid initial="string.printable">
                                <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="global_plot_parameters">
        <section name="plot_parameters" title="Advanced Optional Plot Parameters" expanded="false">
            <param type="float" name="figure_height"
                argument="--height"
                optional="true"
                label="Figure Height (Default 4.5)"
            />
            <param type="float" name="figure_width"
                argument="--width"
                optional="true"
                label="Figure Width (Default 1.5)"
            />
            <param type="float" name="tick_width"
                argument="--tick-width"
                optional="true"
                label="Axis Tick Width (Default 1.5)"
            />
            <param type="text" name="title"
                argument="--title"
                optional="true"
                label="Specify Figure Title">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                </sanitizer>
            </param>
            <param type="text" name="x_label"
                argument="--xlab"
                optional="true"
                label="Specify X-axis label">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                </sanitizer>
            </param>
            <param type="float" name="min_x"
                argument="--x-min"
                optional="true"
                label="Minimum value of X-axis (float)"
            />
            <param type="float" name="max_x"
                argument="--x-max"
                optional="true"
                label="Maximum value of X-axis (float)"
            />
            <param type="text" name="y_label"
                argument="--ylab"
                optional="true"
                label="Specify Y-axis label">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                </sanitizer>
            </param>
            <param type="float" name="min_y"
                argument="--y-min"
                optional="true"
                label="Minimum value of Y-axis (float)"
            />
            <param type="float" name="max_y"
                argument="--y-max"
                optional="true"
                label="Maximum value of Y-axis (float)"
            />
        </section>
    </xml>
    <token name="@HELP_COLUMNS@">
Column Name Input Help
######################

- Multiple names can be given if separated by a ' , '.

    - ex. 'ID,Organism' would target the columns named ID and Organism for the function 

- Column names are case SeNsitive

- Column numbers can also be given:

    -ex. '1,2,3' or '1-3' for inputting columns 1-3.

- You can also specify all but unwanted column(s) with a ' - '.

    - ex. '-ID' would target all columns but the ID column

----
    </token>
    <token name="@HELP_INPUT_DATA@">
Input Data
##########

::

    **Limitations of Input Data**

    1. The CSV parser requires all the lines have same number of fields/columns.
        If your file has illegal rows, set the "Illegal Rows" parameter to "Yes" to pass your data through
        Even lines with spaces will cause error.
        Example bad table below.

    2. By default, csvtk thinks files have header rows. If your file does not, set global parameter
        "Has Header Row" to "No"

    3. Column names should be unique and are case sensitive!

    4. Lines starting with "#" or "$" will be ignored, if in the header row

    5. If " exists in tab-delimited files, set Lazy quotes global parameter to "Yes"

Example bad table:

+--------+--------+--------+--------+
| Head 1 | Head 2 | Head 3 | Head 3 |
+========+========+========+========+
| 1      | 2      | 3      |        |
+--------+--------+--------+--------+
| this   | will   |        | break  |
+--------+--------+--------+--------+

Bad tables may work if both the "Ignore Illegal Rows" and "Ignore Empty Rows" global parameters are set to "Yes",
But there is no guarentee of that!

----
    </token>
    <token name="@HELP_END_STATEMENT@">
More Information
################
For information from the creators of csvtk, please visit their site at: https://bioinf.shenwei.me/csvtk/

Although be aware that some features may not be available and some small changes were made to work with Galaxy.

**Notable changes from their documentation:**

- Cannot specify multiple file header names (IE cannot use "name;username" as a valid column match)

- No single quotes / apostrophes allowed in text inputs
    </token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@ARTICLE{a1,
                title = {csvtk - CSV/TSV Toolkit},
                author = {Wei Shen},
                url = {https://github.com/shenwei356/csvtk}
                }
            }</citation>
        </citations>
    </xml>
</macros>