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comparison fimo.xml @ 5:eca84de658b0 draft

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author iuc
date Fri, 17 Jun 2016 13:15:48 -0400
parents 0fce5521bb96
children cdcc4bb60bc3
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4:cd54079f0f72 5:eca84de658b0
1 <tool id="meme_fimo" name="FIMO" version="4.11.0.2"> 1 <tool id="meme_fimo" name="FIMO" version="4.11.0.3">
2 <description>- Scan a set of sequences for motifs.</description> 2 <description>- Scan a set of sequences for motifs.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="6.9.3">imagemagick</requirement> 4 <requirement type="package" version="6.9.3">imagemagick</requirement>
5 <requirement type="package" version="4.11.0">meme</requirement> 5 <requirement type="package" version="4.11.0">meme</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 mkdir -p output &&
9 python $__tool_directory__/fimo_wrapper.py 10 python $__tool_directory__/fimo_wrapper.py
10 --input_motifs "${input_motifs}" 11 --input_motifs "${input_motifs}"
11 #if str($fasta_type.fasta_type_selector) == 'history': 12 #if str($fasta_type.fasta_type_selector) == 'history':
12 --input_fasta "${fasta_type.input_database}" 13 --input_fasta "${fasta_type.input_database}"
13 #else: 14 #else:
26 #if str($options_type.motifs_cond.motifs_selector) == 'no': 27 #if str($options_type.motifs_cond.motifs_selector) == 'no':
27 #for $motif in $options_type.motifs: 28 #for $motif in $options_type.motifs:
28 --motif "${motif.motif}" 29 --motif "${motif.motif}"
29 #end for 30 #end for
30 #end if 31 #end if
32 --output_separate_motifs ${options_type.output_separate_motifs}
31 --motif_pseudo "${options_type.motif_pseudo}" 33 --motif_pseudo "${options_type.motif_pseudo}"
32 ${options_type.no_qvalue} 34 ${options_type.no_qvalue}
33 ${options_type.norc} 35 ${options_type.norc}
34 ${options_type.parse_genomic_coord} 36 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
37 --parse_genomic_coord 'yes'
38 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
39 #end if
35 #if str($options_type.psp_cond.psp_selector) == 'yes': 40 #if str($options_type.psp_cond.psp_selector) == 'yes':
36 --input_psp "${input_psp}" 41 --input_psp "${input_psp}"
37 #end if 42 #end if
38 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': 43 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
39 --input_prior_dist "${input_prior_dist}" 44 --input_prior_dist "${input_prior_dist}"
97 <repeat name="motifs" title="Limit to specified motif"> 102 <repeat name="motifs" title="Limit to specified motif">
98 <param name="motif" type="text" value="" label="Specify motif by id" /> 103 <param name="motif" type="text" value="" label="Specify motif by id" />
99 </repeat> 104 </repeat>
100 </when> 105 </when>
101 </conditional> 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>
102 <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"/> 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"/>
103 <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)."/> 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)."/>
104 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" /> 113 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
105 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" /> 114 <conditional name="parse_genomic_coord_cond">
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">
120 <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" />
121 </when>
122 <when value="no"/>
123 </conditional>
106 <conditional name="psp_cond"> 124 <conditional name="psp_cond">
107 <param name="psp_selector" type="select" label="Use position-specific priors?"> 125 <param name="psp_selector" type="select" label="Use position-specific priors?">
108 <option value="no" selected="true">No</option> 126 <option value="no" selected="true">No</option>
109 <option value="yes">Yes</option> 127 <option value="yes">Yes</option>
110 </param> 128 </param>
158 </when> 176 </when>
159 </conditional> 177 </conditional>
160 </actions> 178 </actions>
161 </data> 179 </data>
162 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)"> 180 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
163 <actions> 181 <filter>options_type['output_separate_motifs'] == 'no'</filter>
164 <conditional name="fasta_type.fasta_type_selector"> 182 <actions>
165 <when value="cached"> 183 <conditional name="fasta_type.fasta_type_selector">
166 <action type="metadata" name="dbkey"> 184 <when value="cached">
167 <option type="from_data_table" name="all_fasta" column="1" offset="0"> 185 <action type="metadata" name="dbkey">
168 <filter type="param_value" ref="fasta_type.input_database" column="0"/> 186 <option type="from_data_table" name="all_fasta" column="1" offset="0">
169 </option> 187 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
170 </action> 188 </option>
171 </when> 189 </action>
172 </conditional> 190 </when>
173 </actions> 191 </conditional>
174 </data> 192 </actions>
193 </data>
194 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
195 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
196 <filter>options_type['output_separate_motifs'] == 'yes'</filter>
197 </collection>
175 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"> 198 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
176 <actions> 199 <actions>
177 <conditional name="fasta_type.fasta_type_selector"> 200 <conditional name="fasta_type.fasta_type_selector">
178 <when value="cached"> 201 <when value="cached">
179 <action type="metadata" name="dbkey"> 202 <action type="metadata" name="dbkey">
207 <param name="options_type_selector" value="basic"/> 230 <param name="options_type_selector" value="basic"/>
208 <param name="non_commercial_use" value="True"/> 231 <param name="non_commercial_use" value="True"/>
209 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/> 232 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
210 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/> 233 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
211 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/> 234 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
212 <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/> 235 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
213 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/> 236 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
214 </test> 237 </test>
215 <test> 238 <test>
216 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> 239 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
217 <param name="fasta_type_selector" value="history"/> 240 <param name="fasta_type_selector" value="history"/>
219 <param name="options_type_selector" value="advanced"/> 242 <param name="options_type_selector" value="advanced"/>
220 <param name="non_commercial_use" value="True"/> 243 <param name="non_commercial_use" value="True"/>
221 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> 244 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
222 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> 245 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
223 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/> 246 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
224 <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/> 247 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
248 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
249 </test>
250 <test>
251 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
252 <param name="fasta_type_selector" value="history"/>
253 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
254 <param name="options_type_selector" value="advanced"/>
255 <param name="parse_genomic_coord" value="--parse_genomic_coord"/>
256 <param name="remove_duplicate_coords" value="yes"/>
257 <param name="output_separate_motifs" value="yes"/>
258 <param name="non_commercial_use" value="True"/>
259 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
260 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
261 <output_collection name="motifs" type="list">
262 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
263 </output_collection>
264 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
225 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> 265 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
226 </test> 266 </test>
227 </tests> 267 </tests>
228 <help> 268 <help>
229 269
233 Before using, be sure to review, agree, and comply with the license.** 273 Before using, be sure to review, agree, and comply with the license.**
234 274
235 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences). 275 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
236 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of 276 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
237 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold 277 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
238 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable), too. 278 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
239 279
240 .. class:: infomark 280 .. class:: infomark
241 281
242 For detailed information on FIMO, click here_, or view the license_. 282 For detailed information on FIMO, click here_, or view the license_.
243 283