<tool id="gmt_music_pfam" name="gmt_music_pfam">
  <description>
    Add Pfam annotation to a MAF file
  </description>
  <command>
    gmt music pfam --maf-file=$maf_file --output-file=$output_file
  </command>
  <inputs>
    <param name="maf_file" format="maf" type="data" help="" />

  </inputs>
  <outputs>
    <data name="output_file" format="pfam" label="" help="" />

  </outputs>
  <help>
    

**USAGE**

 gmt music pfam --maf-file=? --output-file=?


**SYNOPSIS**

This command adds Pfam Domains to a column at the end of a MAF file.

**EXAMPLE:**
	gmt music pfam --maf-file myMAF.tsv --output-file myMAF.tsv.pfam


**REQUIRED ARGUMENTS**

  maf-file   Text
    List of mutations in MAF format 
  output-file   Text
    MAF file with Pfam domain column appended 


**DESCRIPTION**

 This tool takes a MAF file, determines the location of each variant therein, and then uses a
 fast-lookup to retrieve all of the Pfam annotation domains that the variant crosses. A column is
 appended to the end of the input MAF file called "Pfam_Annotation_Domains" where the results are
 listed. "NA" is listed if no Pfam domains are found.



  </help>
</tool>