comparison column_maker.xml @ 10:aff5135563c6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6

9:6595517c2dd8

<tool id="Add_a_column1" name="Compute" version="2.0">
    <description>on rows</description>
    <macros>
        <xml name="compute_repeat">
            <repeat name="expressions" title="Expressions" min="1" default="1">
                <param name="cond" type="text" value="c3-c2" label="Add expression">

                <yield />
            </repeat>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="3.8">python</requirement>
        <requirement type="package" version="1.23.1">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/column_maker.py'
#if str($error_handling.auto_col_types) == 'on':
    #set $col_types = $input.metadata.column_types

                    <param name="pos" value="1" />
                </conditional>
            </repeat>
            <output name="out_file1" file="column_maker_out4.tab" />
        </test>
        <!-- Test list column type in input -->
        <test>
            <param name="input" value="bed12.bed" ftype="bed12" />
            <!-- get largest blocksize from column 11 of bed12 and use it as
            new score value -->

- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file

- The following built-in Python functions are available for use in expressions::

    abs | all | any | ascii | bin | bool | chr | ceil | complex | divmod

    exp | float | floor | format | hex | int | len | list | log | log10

    list | map | max | min | oct | ord | pow | range | reversed

    round | set | sorted | sqrt | str | sum | type

- In addition the numpy function ``format_float_positional`` is available to
  control the formatting of floating point numbers.

- Expressions can be chained, and the tool will keep track of newly added

**If an expression cannot be computed for a row**: `Fill in a replacement value`

**Replacement value**: `.`
    ]]></help>
    <citations />
</tool>

10:aff5135563c6

<tool id="Add_a_column1" name="Compute" version="2.1" profile="23.0">
    <description>on rows</description>
    <macros>
        <xml name="compute_repeat">
            <repeat name="expressions" title="Expressions" min="1" default="1">
                <param name="cond" type="text" value="c3-c2" label="Add expression">

                <yield />
            </repeat>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="3.12">python</requirement>
        <requirement type="package" version="2.1.0">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/column_maker.py'
#if str($error_handling.auto_col_types) == 'on':
    #set $col_types = $input.metadata.column_types

                    <param name="pos" value="1" />
                </conditional>
            </repeat>
            <output name="out_file1" file="column_maker_out4.tab" />
        </test>
        <test>
            <param name="cond" value="cos(pi)+sin(tau)*c2"/>
            <param name="input" value="1.bed" ftype="bed" />
            <output name="out_file1" file="column_maker_out5.interval"/>
        </test>
        <!-- Test list column type in input -->
        <test>
            <param name="input" value="bed12.bed" ftype="bed12" />
            <!-- get largest blocksize from column 11 of bed12 and use it as
            new score value -->

- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file

- The following built-in Python functions are available for use in expressions::

    abs | all | any | ascii | bin | bool | chr | complex | divmod | float | format | hex | int | len | list 
    map | max | min | oct | ord | pow | range | reversed | round | set | sorted | str | sum | type

    acos | acosh | asin | asinh | atan | atan2 | atanh | cbrt | ceil | comb | copysign | cos | cosh | degrees 
    dist | erf | erfc | exp | exp2 | expm1 | fabs | factorial | floor | fmod | frexp | fsum | gamma | gcd
    hypot | inf | isclose | isfinite | isinf | isnan | isqrt | ldexp | lgamma | log | log10 | log1p | log2
    modf | nextafter | perm | pow | prod | remainder | sin | sqrt | tan | tanh | tau | trunc | ulp

- In addition the numpy function ``format_float_positional`` is available to
  control the formatting of floating point numbers.

- Expressions can be chained, and the tool will keep track of newly added

**If an expression cannot be computed for a row**: `Fill in a replacement value`

**Replacement value**: `.`
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkae410</citation>
    </citations>
</tool>