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/tools/filters/gff/gtf_filter_by_attribute_values_list.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 42 lines | 38 code | 2 blank | 2 comment | 0 complexity | 63b93a76b0309346041a9d5ed3947537 MD5 | raw file
 1<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">
 2    <description></description>
 3    <command interpreter="python">
 4      gtf_filter_by_attribute_values_list.py $input $attribute_name $ids $output
 5    </command>
 6    <inputs>
 7        <param format="gtf" name="input" type="data" label="Filter"/>
 8        <param name="attribute_name" type="select" label="Using attribute name">
 9            <option value="gene_id">gene_id</option>
10            <option value="transcript_id">transcript_id</option>
11            <option value="p_id">p_id</option>
12            <option value="tss_id">tss_id</option>
13        </param>
14        <param format="tabular,txt" name="ids" type="data" label="And attribute values"/>
15    </inputs>
16    <outputs>
17        <data format="gtf" name="output"/>
18    </outputs>
19    <tests>
20        <!-- Test filtering with a simple list of values. -->
21        <test>
22            <param name="input" value="gops_subtract_in1.gff"/>
23            <param name="attribute_name" value="gene_id"/>
24            <param name="ids" value="gtf_filter_by_attribute_values_list_in1.txt"/>
25            <output name="output" file="gtf_filter_by_attribute_values_list_out1.gtf"/>
26        </test>
27        <!-- Test filtering with a more complex tabular file. -->
28        <test>
29            <param name="input" value="gtf_filter_by_attribute_values_list_in2.gtf"/>
30            <param name="attribute_name" value="transcript_id"/>
31            <param name="ids" value="gtf_filter_by_attribute_values_list_in3.tabular"/>
32            <output name="output" file="gtf_filter_by_attribute_values_list_out2.gtf"/>
33        </test>
34    </tests>
35    <help>
36
37This tool filters a GTF file using a list of attribute values. The attribute values are
38taken from the first column in the file; additional columns in the file are ignored. An example
39use of this tool is to filter a GTF file using a list of transcript_ids or gene_ids obtained from Cuffdiff.
40
41    </help>
42</tool>