| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/5.4.1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/5.0.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.1.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.4 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.3 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.0 |
| meme_fimo |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| meme | 5.4.1 | package |
| Additional information about this tool |
#if not $non_commercial_use
>&2 echo "this tool is only available for non commercial use";
exit 1;
#end if
fimo
-o ./out/
$scanrc
#if str( $options_type.options_type_selector ) == 'advanced':
--thresh $options_type.thresh
$options_type.qv_thresh
#if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
--bgfile --motif--
#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
--bgfile $options_type.bgfile_type.bgfile
#elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
--bgfile --uniform--
#end if
$options_type.max_strand
--max-stored-scores $options_type.max_stored_scores
#if str( $options_type.motifs_cond.motif_selector) == 'yes':
#for $motif in $options_type.motifs_cond.motifs:
--motif '$motif.motif'
#end for
#end if
--motif-pseudo $options_type.motif_pseudo
$options_type.no_qvalue
$options_type.parse_genomic_coords
#if str( $options_type.psp_cond.psp_selector ) == 'yes':
--psp $options_type.psp_cond.input_psp
--alpha $options_type.psp_cond.alpha
#end if
#if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
--prior-dist $options_type.prior_dist_cond.input_prior_dist
#end if
#end if
'$input_motifs'
#if str($fasta_type.fasta_type_selector) == 'history':
'${fasta_type.input_database}'
#else:
'${fasta_type.input_database.fields.path}'
#end if
&& mv ./out/fimo.html '${html_outfile}'
&& mv ./out/fimo.tsv '${txt_outfile}'
&& mv ./out/fimo.xml '${xml_outfile}'
&& mv ./out/fimo.gff '${gff_outfile}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_motifs: meme_fimo_input_1.xml fasta_type|input_database: hsa_chrM.fa fasta_type|fasta_type_selector: history scanrc: True options_type|options_type_selector: basic non_commercial_use: True output_options|html_outfile: True output_options|xml_outfile: True output_options|gff_outfile: True |
name: value name: value name: value name: value |
meme_fimo_input_1.xml hsa_chrM.fa value |
| Test-2 |
input_motifs: dreme_fimo_input_1.xml fasta_type|input_database: hsa_chrM.fa fasta_type|fasta_type_selector: history scanrc: True options_type|bgfile_type|bgfile: fimo_background_probs_hsa_chrM.txt options_type|bgfile_type|bgfile_type_selector: bgfile options_type|options_type_selector: advanced non_commercial_use: True output_options|html_outfile: True output_options|xml_outfile: True output_options|gff_outfile: True |
name: value name: value name: value name: value |
dreme_fimo_input_1.xml hsa_chrM.fa fimo_background_probs_hsa_chrM.txt value |
| Test-3 |
input_motifs: dreme_fimo_input_1.xml fasta_type|input_database: hsa_chrM.fa fasta_type|fasta_type_selector: history scanrc: True options_type|thresh: 0.01 options_type|bgfile_type|bgfile_type_selector: uniform_distr options_type|motifs_cond|motifs_0|motif: ACTAAYH options_type|motifs_cond|motif_selector: yes options_type|options_type_selector: advanced non_commercial_use: True output_options|html_outfile: True output_options|xml_outfile: True output_options|gff_outfile: False |
name: value name: value name: value |
dreme_fimo_input_1.xml hsa_chrM.fa value |