<tool id="match" name="match">
  <description>find short motif occurrences</description>
  <command> ./match $motif $seq $output $nmismatch $rc $bed > $log</command>
  <inputs>
    
    <param name="motif" type="data" format="fasta" label="Search occurances of the following motifs" help="one or multiple sequences, FASTA format"/>         
    <param name="seq" type="data" format="fasta" label="in sequences" help="one or multiple sequences, FASTA format"/>   
      <param name="nmismatch" size="10" type="integer" value="0" label="number of mismatches allowed"/>
    <param name="rc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="norc" falsevalue="rc" checked="False"/>
        <param name="bed" label="output BED format" help="Default is tabular file (see example below). Please only check this if your sequence identifier looks like: hg18_chr6_122208322_122209078_+ (true for galaxy tool extracted sequences)" type="boolean" truevalue="bed" falsevalue="nobed" checked="True"/>
  </inputs>
  <outputs>
    <data format="log" name="log" label="${tool.name} on ${on_string} (log)"/>
    <data format="bed" name="outfile" label="${tool.name} on ${on_string} (bed)"/>
  </outputs>
  <help>

**What it does**

This tool searches occurrences of a short nucleotide seuqences (allowing mismatches) in a set of longer sequences.

Example motif file::

    >motif1
    CAGGTAAGT
    >motif2
    GTTTGGGGGCC
    
Example sequence file::

    >hg18_chr6_122208322_122209078_+
    CGTCGTAGCTACTAGCTACGTACGTACGTAGCTAGCATGCATGCTACGTA
    CGTAGCTAGCTAAAAAAAAAAAAAAACTGCGGCTAGCTAGCTAGCTACGT
    CGATCGTAGCTAC...
    >hg18_chr6_1208322_122209023_+
    CGATGCTAGCTAGCTAGCTACGTAGCTAGCTAGTCGATGCTAGCTAGCTA     
    ATGCTAGCTAGC....
    
Output (bed)::

    chr11	72790893	72790902	ACTTAACTG	1	-	antisense	5ss,G4T:CAGTTAAGT-rc	hg18_chr11_727
90846_72791902_+	47
    chr11	72791880	72791889	CAGGTAAGA	1	+	sense	5ss,T9A:CAGGTAAGA	hg18_chr11_72790846_72
791902_+	1034


Output (tab)::

    Tmod4	802	5ss:CAGGTAAGT-rc	ACTTACCTG
    Atp7b	77	5ss:CAGGTAAGT	CAGGTAAGT
    Fnta	665	5ss:CAGGTAAGT	CAGGTAAGT



  </help>
</tool>