|
6
|
1 <tool id="meme_fimo" name="FIMO" version="4.11.1.0">
|
|
0
|
2 <description>- Scan a set of sequences for motifs.</description>
|
|
|
3 <requirements>
|
|
6
|
4 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
|
|
|
5 <requirement type="package" version="4.11.1">meme</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 <![CDATA[
|
|
|
9 mkdir -p output &&
|
|
|
10 python $__tool_directory__/fimo_wrapper.py
|
|
|
11 --input_motifs "${input_motifs}"
|
|
|
12 #if str($fasta_type.fasta_type_selector) == 'history':
|
|
|
13 --input_fasta "${fasta_type.input_database}"
|
|
|
14 #else:
|
|
|
15 --input_fasta "${fasta_type.input_database.fields.path}"
|
|
|
16 #end if
|
|
|
17 --options_type $options_type.options_type_selector
|
|
|
18 #if str($options_type.options_type_selector) == 'advanced':
|
|
|
19 --alpha "${options_type.alpha}"
|
|
|
20 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
|
|
|
21 --bgfile "motif-file"
|
|
|
22 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
|
|
|
23 --bgfile "${options_type.bgfile_type.bgfile}"
|
|
|
24 #end if
|
|
|
25 ${options_type.max_strand}
|
|
|
26 --max_stored_scores "${options_type.max_stored_scores}"
|
|
|
27 #if str($options_type.motifs_cond.motifs_selector) == 'no':
|
|
|
28 #for $motif in $options_type.motifs:
|
|
|
29 --motif "${motif.motif}"
|
|
|
30 #end for
|
|
|
31 #end if
|
|
|
32 --output_separate_motifs ${options_type.output_separate_motifs}
|
|
|
33 --motif_pseudo "${options_type.motif_pseudo}"
|
|
|
34 ${options_type.no_qvalue}
|
|
|
35 ${options_type.norc}
|
|
4
|
36 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
|
|
|
37 --parse_genomic_coord 'yes'
|
|
0
|
38 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
|
|
|
39 #end if
|
|
|
40 #if str($options_type.psp_cond.psp_selector) == 'yes':
|
|
|
41 --input_psp "${input_psp}"
|
|
|
42 #end if
|
|
|
43 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
|
|
|
44 --input_prior_dist "${input_prior_dist}"
|
|
|
45 #end if
|
|
|
46 ${options_type.qv_thresh}
|
|
|
47 --thresh ${options_type.thresh}
|
|
|
48 #end if
|
|
|
49 --output_path '${html_outfile.files_path}'
|
|
|
50 --html_output "${html_outfile}"
|
|
|
51 --interval_output '${interval_outfile}'
|
|
|
52 --txt_output "${txt_outfile}"
|
|
|
53 --xml_output "${xml_outfile}"
|
|
|
54 --gff_output "${gff_outfile}"
|
|
|
55 ]]>
|
|
|
56 </command>
|
|
|
57 <inputs>
|
|
|
58 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
|
|
|
59 <conditional name="fasta_type">
|
|
|
60 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
|
|
|
61 <option value="cached">Locally Cached sequences</option>
|
|
|
62 <option value="history" selected="true">Sequences from your history</option>
|
|
|
63 </param>
|
|
|
64 <when value="cached">
|
|
|
65 <param name="input_database" type="select" label="Genome to search">
|
|
|
66 <options from_data_table="all_fasta" />
|
|
|
67 </param>
|
|
|
68 </when>
|
|
|
69 <when value="history">
|
|
|
70 <param format="fasta" name="input_database" type="data" label="Sequences"/>
|
|
|
71 </when>
|
|
|
72 </conditional>
|
|
|
73 <conditional name="options_type">
|
|
|
74 <param name="options_type_selector" type="select" label="Options configuration">
|
|
|
75 <option value="basic" selected="true">Basic</option>
|
|
|
76 <option value="advanced">Advanced</option>
|
|
|
77 </param>
|
|
|
78 <when value="basic" />
|
|
|
79 <when value="advanced">
|
|
|
80 <param name="alpha" type="float" value="1.0" min="0" max="1.0" label="Alpha parameter for calculating position specific priors" help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)."/>
|
|
|
81 <conditional name="bgfile_type">
|
|
|
82 <param name="bgfile_type_selector" type="select" label="Background file type">
|
|
|
83 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
|
|
|
84 <option value="motif_file">Use frequencies from motif file</option>
|
|
|
85 <option value="bgfile">Use frequencies from background file</option>
|
|
|
86 </param>
|
|
|
87 <when value="motif_file" />
|
|
|
88 <when value="default" />
|
|
|
89 <when value="bgfile">
|
|
|
90 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/>
|
|
|
91 </when>
|
|
|
92 </conditional>
|
|
|
93 <param name="max_strand" label="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score" type="boolean" truevalue="--max_strand" falsevalue="" checked="False" help="If the scores are tied, the matching strand is chosen at random. Leave unchecked to report both matches."/>
|
|
|
94 <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
|
|
|
95 <conditional name="motifs_cond">
|
|
|
96 <param name="motifs_selector" type="select" label="Use all motifs in input?">
|
|
|
97 <option value="yes" selected="true">Yes</option>
|
|
|
98 <option value="no">No</option>
|
|
|
99 </param>
|
|
|
100 <when value="yes"/>
|
|
|
101 <when value="no">
|
|
|
102 <repeat name="motifs" title="Limit to specified motif">
|
|
|
103 <param name="motif" type="text" value="" label="Specify motif by id" />
|
|
|
104 </repeat>
|
|
|
105 </when>
|
|
|
106 </conditional>
|
|
|
107 <param name="output_separate_motifs" type="select" label="Output a dataset per motif?" help="Output a collection consisting of a separate dataset for each motif in the input">
|
|
|
108 <option value="no" selected="true">No</option>
|
|
|
109 <option value="yes">Yes</option>
|
|
|
110 </param>
|
|
|
111 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
|
|
|
112 <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/>
|
|
|
113 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
|
|
|
114 <conditional name="parse_genomic_coord_cond">
|
|
4
|
115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
|
|
|
116 <option value="no" selected="true">No</option>
|
|
|
117 <option value="yes">Yes</option>
|
|
|
118 </param>
|
|
|
119 <when value="yes">
|
|
6
|
120 <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
|
|
|
121 <option value="no" selected="true">No</option>
|
|
|
122 <option value="yes">Yes</option>
|
|
|
123 </param>
|
|
0
|
124 </when>
|
|
4
|
125 <when value="no"/>
|
|
0
|
126 </conditional>
|
|
|
127 <conditional name="psp_cond">
|
|
|
128 <param name="psp_selector" type="select" label="Use position-specific priors?">
|
|
|
129 <option value="no" selected="true">No</option>
|
|
|
130 <option value="yes">Yes</option>
|
|
|
131 </param>
|
|
|
132 <when value="no"/>
|
|
|
133 <when value="yes">
|
|
|
134 <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/>
|
|
|
135 </when>
|
|
|
136 </conditional>
|
|
|
137 <conditional name="prior_dist_cond">
|
|
|
138 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
|
|
|
139 <option value="no" selected="true">No</option>
|
|
|
140 <option value="yes">Yes</option>
|
|
|
141 </param>
|
|
|
142 <when value="no"/>
|
|
|
143 <when value="yes">
|
|
|
144 <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/>
|
|
|
145 </when>
|
|
|
146 </conditional>
|
|
|
147 <param name="qv_thresh" label="Use q-values for the output threshold" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" help="Leave unchecked to use p-values for the output threshold."/>
|
|
|
148 <param name="thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only search results with a p-value less than the threshold will be output. The threshold can be set to use q-values rather than p-values via the option above."/>
|
|
|
149 </when>
|
|
|
150 </conditional>
|
|
|
151 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
|
|
|
152 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
|
|
|
153 </param>
|
|
|
154 </inputs>
|
|
|
155 <outputs>
|
|
|
156 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
|
|
|
157 <actions>
|
|
|
158 <conditional name="fasta_type.fasta_type_selector">
|
|
|
159 <when value="cached">
|
|
|
160 <action type="metadata" name="dbkey">
|
|
|
161 <option type="from_data_table" name="all_fasta" column="1" offset="0">
|
|
|
162 <filter type="param_value" column="0" value="seq" keep="True"/>
|
|
|
163 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
|
|
|
164 </option>
|
|
|
165 </action>
|
|
|
166 </when>
|
|
|
167 </conditional>
|
|
|
168 </actions>
|
|
|
169 </data>
|
|
|
170 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
|
|
|
171 <actions>
|
|
|
172 <conditional name="fasta_type.fasta_type_selector">
|
|
|
173 <when value="cached">
|
|
|
174 <action type="metadata" name="dbkey">
|
|
|
175 <option type="from_data_table" name="all_fasta" column="1" offset="0">
|
|
|
176 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
|
|
|
177 </option>
|
|
|
178 </action>
|
|
|
179 </when>
|
|
|
180 </conditional>
|
|
|
181 </actions>
|
|
|
182 </data>
|
|
|
183 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
|
|
6
|
184 <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter>
|
|
0
|
185 <actions>
|
|
|
186 <conditional name="fasta_type.fasta_type_selector">
|
|
|
187 <when value="cached">
|
|
|
188 <action type="metadata" name="dbkey">
|
|
|
189 <option type="from_data_table" name="all_fasta" column="1" offset="0">
|
|
|
190 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
|
|
|
191 </option>
|
|
|
192 </action>
|
|
|
193 </when>
|
|
|
194 </conditional>
|
|
|
195 </actions>
|
|
|
196 </data>
|
|
|
197 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
|
|
|
198 <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="gff" visible="false" />
|
|
6
|
199 <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
|
|
0
|
200 </collection>
|
|
|
201 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
|
|
|
202 <actions>
|
|
|
203 <conditional name="fasta_type.fasta_type_selector">
|
|
|
204 <when value="cached">
|
|
|
205 <action type="metadata" name="dbkey">
|
|
|
206 <option type="from_data_table" name="all_fasta" column="1" offset="0">
|
|
|
207 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
|
|
|
208 </option>
|
|
|
209 </action>
|
|
|
210 </when>
|
|
|
211 </conditional>
|
|
|
212 </actions>
|
|
|
213 </data>
|
|
|
214 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
|
|
|
215 <actions>
|
|
|
216 <conditional name="fasta_type.fasta_type_selector">
|
|
|
217 <when value="cached">
|
|
|
218 <action type="metadata" name="dbkey">
|
|
|
219 <option type="from_data_table" name="all_fasta" column="1" offset="0">
|
|
|
220 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
|
|
|
221 </option>
|
|
|
222 </action>
|
|
|
223 </when>
|
|
|
224 </conditional>
|
|
|
225 </actions>
|
|
|
226 </data>
|
|
|
227 </outputs>
|
|
|
228 <tests>
|
|
|
229 <test>
|
|
|
230 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
|
|
|
231 <param name="fasta_type_selector" value="history"/>
|
|
|
232 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
|
|
|
233 <param name="options_type_selector" value="basic"/>
|
|
|
234 <param name="non_commercial_use" value="True"/>
|
|
|
235 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
|
|
|
236 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
|
|
|
237 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
|
|
4
|
238 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
|
|
0
|
239 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
|
|
|
240 </test>
|
|
|
241 <test>
|
|
|
242 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
|
|
|
243 <param name="fasta_type_selector" value="history"/>
|
|
|
244 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
|
|
|
245 <param name="options_type_selector" value="advanced"/>
|
|
|
246 <param name="non_commercial_use" value="True"/>
|
|
|
247 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
|
|
|
248 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
|
|
|
249 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
|
|
4
|
250 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
|
|
0
|
251 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
|
|
|
252 </test>
|
|
|
253 <test>
|
|
|
254 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
|
|
|
255 <param name="fasta_type_selector" value="history"/>
|
|
|
256 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
|
|
|
257 <param name="options_type_selector" value="advanced"/>
|
|
|
258 <param name="parse_genomic_coord" value="--parse_genomic_coord"/>
|
|
|
259 <param name="remove_duplicate_coords" value="yes"/>
|
|
|
260 <param name="output_separate_motifs" value="yes"/>
|
|
|
261 <param name="non_commercial_use" value="True"/>
|
|
|
262 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
|
|
|
263 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
|
|
|
264 <output_collection name="motifs" type="list">
|
|
4
|
265 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
|
|
0
|
266 </output_collection>
|
|
4
|
267 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
|
|
0
|
268 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
|
|
|
269 </test>
|
|
|
270 </tests>
|
|
|
271 <help>
|
|
|
272
|
|
|
273 .. class:: warningmark
|
|
|
274
|
|
|
275 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
|
|
|
276 Before using, be sure to review, agree, and comply with the license.**
|
|
|
277
|
|
|
278 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
|
|
|
279 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
|
|
|
280 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
|
|
|
281 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
|
|
|
282
|
|
|
283 .. class:: infomark
|
|
|
284
|
|
|
285 For detailed information on FIMO, click here_, or view the license_.
|
|
|
286
|
|
|
287 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
|
|
|
288 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
|
|
|
289
|
|
|
290 </help>
|
|
|
291 <citations>
|
|
|
292 <citation type="doi">10.1093/bioinformatics/btr064</citation>
|
|
|
293 </citations>
|
|
|
294 </tool>
|
