galaxy-central / tools / filters / gff / gtf_filter_by_attribute_values_list.xml

<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">
    <command interpreter="python"> $input $attribute_name $ids $output
        <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 format="tabular,txt" name="ids" type="data" label="And attribute values"/>
        <data format="gtf" name="output"/>
        <!-- Test filtering with a simple list of values. -->
            <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 filtering with a more complex tabular file. -->
            <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"/>

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.