<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">

    <description></description>

    <command interpreter="python">

      gtf_filter_by_attribute_values_list.py $input $attribute_name $ids $output

    </command>

    <inputs>

        <param format="gtf" name="input" type="data" label="Filter"/>

        <param name="attribute_name" type="select" label="Using attribute name">

            <option value="gene_id">gene_id</option>

            <option value="transcript_id">transcript_id</option>

            <option value="p_id">p_id</option>

            <option value="tss_id">tss_id</option>

        </param>

        <param format="tabular,txt" name="ids" type="data" label="And attribute values"/>

    </inputs>

    <outputs>

        <data format="gtf" name="output"/>

    </outputs>

    <tests>

        <!-- Test filtering with a simple list of values. -->

        <test>

            <param name="input" value="gops_subtract_in1.gff"/>

            <param name="attribute_name" value="gene_id"/>

            <param name="ids" value="gtf_filter_by_attribute_values_list_in1.txt"/>

            <output name="output" file="gtf_filter_by_attribute_values_list_out1.gtf"/>

        </test>

        <!-- Test filtering with a more complex tabular file. -->

        <test>

            <param name="input" value="gtf_filter_by_attribute_values_list_in2.gtf"/>

            <param name="attribute_name" value="transcript_id"/>

            <param name="ids" value="gtf_filter_by_attribute_values_list_in3.tabular"/>

            <output name="output" file="gtf_filter_by_attribute_values_list_out2.gtf"/>

        </test>

    </tests>

    <help>



This tool filters a GTF file using a list of attribute values. The attribute values are

taken from the first column in the file; additional columns in the file are ignored. An example

use of this tool is to filter a GTF file using a list of transcript_ids or gene_ids obtained from Cuffdiff.



    </help>

</tool>