annotate dbkit_create.xml @ 3:3b449f158132 draft default tip

"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"

<tool id="ffindex_dbkit_create" name="DBKit Create" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
    <description>database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    mkdir -p inputs &&
    #for item in $inputs
        ln -s '${item}' 'inputs/${item.element_identifier}' &&
    #end for
    dbkit_create.py
        -l '$input'
        -p 'inputs'
        -o '$index'
        -d '$database'
        -g '$log'
        -il '$advanced.idlength'
        -ic '$advanced.idcase'
        -ie '$advanced.idextension'
        -ip '$advanced.idprefix'
    ]]>    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." />
        <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." />
        <conditional name="advanced">
            <param name="type" type="select" label="Identifier Formatting Options" help="">
                <option value="true">Yes, I want to format my identifiers</option>
                <option value="false">No formatting</option>
            </param>
            <when value="true">
                <param name="idprefix" type="text" optional="true" label="Identifier Prefix" help="Specify the prefix of the identifier">
                    <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator>
                </param>
                <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier">
                    <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator>
                </param>
                <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)." />
                <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional).">
                    <option value="">Unformatted</option>
                    <option value="lower">Lower</option>
                    <option value="upper">Upper</option>
                </param>
            </when>
            <when value="false">
                <param name="idprefix" type="hidden" value="" />
                <param name="idextension" type="hidden" value="" />
                <param name="idlength" type="hidden" value="0" />
                <param name="idcase" type="hidden" value="" />
            </when>
        </conditional>
        <expand macro="logfile" />
    </inputs>
    <outputs>
        <data name="index" format="ffindex" label="DBKit Index" />
        <data name="database" format="ffdata" label="DBKit Database" />
        <data format="txt" name="log" label="DBKit Log">
            <filter>logfile</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="create/sequences.tabular" ftype="tabular" />
            <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" />
            <conditional name="advanced">
                <param name="type" value="false" />
            </conditional>
            <output name="index" file="create/sequences.ffindex" ftype="ffindex" />
            <output name="database" file="create/sequences.ffdata" ftype="ffdata" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
    ]]>    </help>
    <expand macro="citations" />
</tool>