view pfam_search/pfam_filter.xml @ 0:68a3648c7d91 draft default tip

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<tool id="pfam_Filter" name="PFAM search" version="0.">
 <description>keyword search on PFAM annotations</description>
 <command> /home/inmare/galaxy/tools/pfam_search/annota.Filter.pl $prot $pfam $out $search</command>
 <description> "approved by the boss" </description>
 <inputs>
 	<param name="prot" type="data" format="fasta" label="protein file used as input with pfamScan" help="fasta only"/>
 	<param name="pfam" type="data" format="tabular" label="pfamScan output" help="this file should match the protein file"/>
 	<param name="search" type="text" label="regular expression to search" help="case sensitive!"/>  
 </inputs>
 <outputs>
 	<data name="out" ftype="tabular" format="html" label="annotated pfam file"/>
 </outputs>
 <test/>
 <help>
	This tool performs keyword searches in order to facilitate the retrieval of proteins containing functional domains of interest from a PFAM annotation. Keyword searches are performed through a simple Perl script implementing exact searches of user specified keywords within the description of each PFAM domain as reported in the clans.txt or pfam.txt domain description files.  Searches can be performed using logical connectors, AND, OR and NOT.  When multiple keywords are entered, the default is to use the AND connector. 
 </help>
</tool>