meme- Find Individual Motif Occurrencesfimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
#if str( $options_type.options_type_selector ) == 'advanced':
--max-seq-length "${options_type.max_seq_length}"
--max-stored-scores "${options_type.max_stored_scores }"
--motif-pseudo "${options_type.motif_pseudo}"
${options_type.norc}
--output-pthresh "${options_type.output_pthresh}"
#for $motif in $options_type.motifs:
--motif "${motif.motif}"
#end for
#if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
--bgfile "motif-file"
#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
--bgfile "${options_type.bgfile_type.bgfile}"
#end if
#if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
--no-qvalue
#else:
--output-qthresh "${options_type.qvalue_type.output_qthresh}"
#end if
#end if
"${input_motifs}"
#if str( $fasta_type.fasta_type_selector ) == 'history':
"${fasta_type.input_database}"
#else:
"${fasta_type.input_database.fields.path}"
#end if
'
'${html_outfile.files_path}'
'${html_outfile}'
'${interval_outfile}'
'${txt_outfile}'
'${xml_outfile}'
'${gff_outfile}'
value == True
.. class:: warningmark
**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
.. class:: infomark
**To cite FIMO:**
`Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. <http://www.ncbi.nlm.nih.gov/pubmed/21330290>`_
For detailed information on FIMO, click here_. To view the license_.
------
**Citation**
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
.. _here: http://meme.nbcr.net/meme/fimo-intro.html
.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html