gff_id_editing.xml

<tool id="gff_id_editing" name="GFF ID editing" version="@VERSION@">
    
    <description>
    <![CDATA[
        Adds ID tags to every gff entry.
    ]]>
    </description>
    
    <macros>
        <import>gff_sqlite_tool_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    
    <version_command>python gff_id_editing.py --version</version_command>
    
    <command interpreter="python">
    <![CDATA[
        
      gff_id_editing.py 
            #if $old_gff and $old_gff is not None:
                --old_gff "$old_gff"
            #end if
        
            #if $new_gff and $new_gff is not None:
                --new_gff "$new_gff"
            #end if
        
    ]]>
    </command>
    
    <inputs>
        <param name="old_gff" type="data" format="gff" label="Input GFF file" help="(--old_gff)" />
    </inputs>
    
    <outputs>
        <data name="new_gff" format="gff" label="GFF data of ${tool.name} on ${on_string}" />
    </outputs>
    
    <tests>
        <test>
            <param name="old_gff" value="FlyBase.gff" />
            <output name="new_gff" file="FlyBaseID.gff" />
        </test>
    </tests>
    
    <help>
<![CDATA[

**Overview**

Gff_id_editing is designed to add ID tags to every entry of a GFF file.
For creating an arbitrary ID, an entry needs at least a parent tag, declared as 'Parent=' or 'parent='.
This tool uses the value of the parent tag, concatenates it with the feature type of the entry and adds a counter for getting unique IDs.
The feature type will be added with ':' and the counting number will be added with '_'.
When encountering multiple parents separated by commas, the tool replaces them with '-' and uses the whole resulting string as the tag prefix.
If the tool finds neither ID nor Parent (or parent) for the tag, it uses 'noParNoID:<feature>_<counter>' as ID.

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**Input**

The input file has to be a GFF file.

------

**Output**

The output will be a GFF file.

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**gff_id_editing parameter list**

The standalone, command-line version of gff_id_editing uses the following parameters::

        --old_gff   [input GFF file name {gff}]
        --new_gff   [output GFF file name {gff}]
        --version   version number

@CITATION@

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