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comparison fimo.xml @ 0:27c742760a84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 16:59:48 -0500
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children 1562b160210d
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-1:000000000000 0:27c742760a84
1 <tool id="meme_fimo" name="FIMO" version="4.11.0.0">
2 <description>- Scan a set of sequences for motifs.</description>
3 <requirements>
4 <requirement type="package" version="4.11.0.0">meme</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 python $__tool_directory__/fimo_wrapper.py
9 --input_motifs "${input_motifs}"
10 #if str($fasta_type.fasta_type_selector) == 'history':
11 --input_fasta "${fasta_type.input_database}"
12 #else:
13 --input_fasta "${fasta_type.input_database.fields.path}"
14 #end if
15 --options_type $options_type.options_type_selector
16 #if str($options_type.options_type_selector) == 'advanced':
17 --alpha "${options_type.alpha}"
18 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
19 --bgfile "motif-file"
20 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
21 --bgfile "${options_type.bgfile_type.bgfile}"
22 #end if
23 ${options_type.max_strand}
24 --max_stored_scores "${options_type.max_stored_scores}"
25 #if str($options_type.motifs_cond.motifs_selector) == 'no':
26 #for $motif in $options_type.motifs:
27 --motif "${motif.motif}"
28 #end for
29 #end if
30 --motif_pseudo "${options_type.motif_pseudo}"
31 ${options_type.no_qvalue}
32 ${options_type.norc}
33 ${options_type.parse_genomic_coord}
34 #if str($options_type.psp_cond.psp_selector) == 'yes':
35 --input_psp "${input_psp}"
36 #end if
37 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
38 --input_prior_dist "${input_prior_dist}"
39 #end if
40 ${options_type.qv_thresh}
41 --thresh ${options_type.thresh}
42 #end if
43 --output_path '${html_outfile.files_path}'
44 --html_output "${html_outfile}"
45 --interval_output '${interval_outfile}'
46 --txt_output "${txt_outfile}"
47 --xml_output "${xml_outfile}"
48 --gff_output "${gff_outfile}"
49 ]]>
50 </command>
51 <inputs>
52 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
53 <conditional name="fasta_type">
54 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
55 <option value="cached">Locally Cached sequences</option>
56 <option value="history" selected="true">Sequences from your history</option>
57 </param>
58 <when value="cached">
59 <param name="input_database" type="select" label="Genome to search">
60 <options from_data_table="all_fasta" />
61 </param>
62 </when>
63 <when value="history">
64 <param format="fasta" name="input_database" type="data" label="Sequences"/>
65 </when>
66 </conditional>
67 <conditional name="options_type">
68 <param name="options_type_selector" type="select" label="Options configuration">
69 <option value="basic" selected="true">Basic</option>
70 <option value="advanced">Advanced</option>
71 </param>
72 <when value="basic" />
73 <when value="advanced">
74 <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)."/>
75 <conditional name="bgfile_type">
76 <param name="bgfile_type_selector" type="select" label="Background file type">
77 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
78 <option value="motif_file">Use frequencies from motif file</option>
79 <option value="bgfile">Use frequencies from background file</option>
80 </param>
81 <when value="motif_file" />
82 <when value="default" />
83 <when value="bgfile">
84 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/>
85 </when>
86 </conditional>
87 <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."/>
88 <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
89 <conditional name="motifs_cond">
90 <param name="motifs_selector" type="select" label="Use all motifs in input?">
91 <option value="yes" selected="true">Yes</option>
92 <option value="no">No</option>
93 </param>
94 <when value="yes"/>
95 <when value="no">
96 <repeat name="motifs" title="Limit to specified motif">
97 <param name="motif" type="text" value="" label="Specify motif by id" />
98 </repeat>
99 </when>
100 </conditional>
101 <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"/>
102 <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)."/>
103 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
104 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" />
105 <conditional name="psp_cond">
106 <param name="psp_selector" type="select" label="Use position-specific priors?">
107 <option value="no" selected="true">No</option>
108 <option value="yes">Yes</option>
109 </param>
110 <when value="no"/>
111 <when value="yes">
112 <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/>
113 </when>
114 </conditional>
115 <conditional name="prior_dist_cond">
116 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
117 <option value="no" selected="true">No</option>
118 <option value="yes">Yes</option>
119 </param>
120 <when value="no"/>
121 <when value="yes">
122 <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/>
123 </when>
124 </conditional>
125 <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."/>
126 <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."/>
127 </when>
128 </conditional>
129 <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">
130 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
131 </param>
132 </inputs>
133 <outputs>
134 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
135 <actions>
136 <conditional name="fasta_type.fasta_type_selector">
137 <when value="cached">
138 <action type="metadata" name="dbkey">
139 <option type="from_data_table" name="all_fasta" column="1" offset="0">
140 <filter type="param_value" column="0" value="seq" keep="True"/>
141 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
142 </option>
143 </action>
144 </when>
145 </conditional>
146 </actions>
147 </data>
148 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
149 <actions>
150 <conditional name="fasta_type.fasta_type_selector">
151 <when value="cached">
152 <action type="metadata" name="dbkey">
153 <option type="from_data_table" name="all_fasta" column="1" offset="0">
154 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
155 </option>
156 </action>
157 </when>
158 </conditional>
159 </actions>
160 </data>
161 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
162 <actions>
163 <conditional name="fasta_type.fasta_type_selector">
164 <when value="cached">
165 <action type="metadata" name="dbkey">
166 <option type="from_data_table" name="all_fasta" column="1" offset="0">
167 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
168 </option>
169 </action>
170 </when>
171 </conditional>
172 </actions>
173 </data>
174 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
175 <actions>
176 <conditional name="fasta_type.fasta_type_selector">
177 <when value="cached">
178 <action type="metadata" name="dbkey">
179 <option type="from_data_table" name="all_fasta" column="1" offset="0">
180 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
181 </option>
182 </action>
183 </when>
184 </conditional>
185 </actions>
186 </data>
187 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
188 <actions>
189 <conditional name="fasta_type.fasta_type_selector">
190 <when value="cached">
191 <action type="metadata" name="dbkey">
192 <option type="from_data_table" name="all_fasta" column="1" offset="0">
193 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
194 </option>
195 </action>
196 </when>
197 </conditional>
198 </actions>
199 </data>
200 </outputs>
201 <tests>
202 <test>
203 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
204 <param name="fasta_type_selector" value="history"/>
205 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
206 <param name="options_type_selector" value="basic"/>
207 <param name="non_commercial_use" value="True"/>
208 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
209 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
210 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
211 <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/>
212 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
213 </test>
214 <test>
215 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
216 <param name="fasta_type_selector" value="history"/>
217 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
218 <param name="options_type_selector" value="advanced"/>
219 <param name="non_commercial_use" value="True"/>
220 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
221 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
222 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
223 <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/>
224 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
225 </test>
226 </tests>
227 <help>
228
229 .. class:: warningmark
230
231 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
232 Before using, be sure to review, agree, and comply with the license.**
233
234 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
235 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
236 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
237 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable), too.
238
239 .. class:: infomark
240
241 For detailed information on FIMO, click here_, or view the license_.
242
243 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
244 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
245
246 </help>
247 <citations>
248 <citation type="doi">10.1093/bioinformatics/btr064</citation>
249 </citations>
250 </tool>