Mercurial > repos > xuebing > sharplabtool
view tools/filters/gff/gtf_filter_by_attribute_values_list.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
line wrap: on
line source
<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="input" name="output" metadata_source="input"/> </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>