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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
author iuc
date Thu, 29 Aug 2024 10:20:10 +0000
parents 19237efe98d1
children
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18:19237efe98d1 19:7ce0fe11b411
1 <tool id="meme_meme" name="MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="meme_meme" name="MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Multiple EM for Motif Elicitation</description> 2 <description>- Multiple EM for Motif Elicitation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">meme_meme</xref> 7 <xref type="bio.tools">meme_meme</xref>
5 </xrefs> 8 </xrefs>
6 <macros> 9 <expand macro="requirements"/>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @CHECK_NON_COMMERCIAL_USE@ 11 @CHECK_NON_COMMERCIAL_USE@
12 export TMPDIR=\${TMPDIR:-.}; 12 export TMPDIR=\${TMPDIR:-.};
13 13
14 meme '$input1' 14 meme '$input1'
79 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}' 79 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}'
80 && mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}' 80 && mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}'
81 && mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}' 81 && mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}'
82 ]]></command> 82 ]]></command>
83 <inputs> 83 <inputs>
84 <param format="fasta" name="input1" type="data" label="Sequences"/> 84 <param name="input1" type="data" format="fasta" label="Sequences"/>
85 <conditional name="options_type"> 85 <conditional name="options_type">
86 <param name="options_type_selector" type="select" label="Options Configuration"> 86 <param name="options_type_selector" type="select" label="Options Configuration">
87 <option value="basic" selected="true">Basic</option> 87 <option value="basic" selected="true">Basic</option>
88 <option value="advanced">Advanced</option> 88 <option value="advanced">Advanced</option>
89 </param> 89 </param>
90 <when value="basic" /> 90 <when value="basic"/>
91 <when value="advanced"> 91 <when value="advanced">
92 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/> 92 <param argument="-sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set"/>
93 <conditional name="alphabet_type"> 93 <conditional name="alphabet_type">
94 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet"> 94 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
95 <option value="protein">Protein</option> 95 <option value="protein">Protein</option>
96 <option value="dna" selected="true">DNA</option> 96 <option value="dna" selected="true">DNA</option>
97 </param> 97 </param>
98 <when value="protein"> 98 <when value="protein">
99 <conditional name="prior_type"> 99 <conditional name="prior_type">
100 <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior"> 100 <param name="prior_type_selector" argument="-prior" type="select" label="Choice of prior">
101 <option value="dirichlet">simple Dirichlet prior</option> 101 <option value="dirichlet">simple Dirichlet prior</option>
102 <option value="dmix" selected="true">mixture of Dirichlets prior</option> 102 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
103 <option value="mega">extremely low variance dmix</option> 103 <option value="mega">extremely low variance dmix</option>
104 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option> 104 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
105 <option value="addone">add +1 to each observed count</option> 105 <option value="addone">add +1 to each observed count</option>
106 </param> 106 </param>
107 <when value="dirichlet"> 107 <when value="dirichlet">
108 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/> 108 <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
109 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 109 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
110 </when> 110 </when>
111 <when value="dmix"> 111 <when value="dmix">
112 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 112 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
113 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 113 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
114 </when> 114 </when>
115 <when value="mega"> 115 <when value="mega">
116 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 116 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
117 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 117 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
118 </when> 118 </when>
119 <when value="megap"> 119 <when value="megap">
120 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 120 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
121 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 121 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
122 </when> 122 </when>
123 <when value="addone" /> 123 <when value="addone"/>
124 </conditional> 124 </conditional>
125 <conditional name="spmap_type"> 125 <conditional name="spmap_type">
126 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap"> 126 <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
127 <option value="uni">uni</option> 127 <option value="uni">uni</option>
128 <option value="pam" selected="true">pam</option> 128 <option value="pam" selected="true">pam</option>
129 <option value="cons">Use starting point from string</option> 129 <option value="cons">Use starting point from string</option>
130 </param> 130 </param>
131 <when value="uni"> 131 <when value="uni">
132 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/> 132 <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
133 </when> 133 </when>
134 <when value="pam"> 134 <when value="pam">
135 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/> 135 <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
136 </when> 136 </when>
137 <when value="cons"> 137 <when value="cons">
138 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/> 138 <param argument="-cons" type="text" value="" label="Starting point from string"/>
139 </when> 139 </when>
140 </conditional> 140 </conditional>
141 </when> 141 </when>
142 <when value="dna"> 142 <when value="dna">
143 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/> 143 <param argument="-revcomp" type="boolean" truevalue="-revcomp" falsevalue="" checked="False" label="Check reverse complement"/>
144 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/> 144 <param argument="-pal" type="boolean" truevalue="-pal" falsevalue="" checked="False" label="Check for palindromes"/>
145 <conditional name="prior_type"> 145 <conditional name="prior_type">
146 <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior"> 146 <param name="prior_type_selector" argument="-prior" type="select" label="Sequence Alphabet">
147 <option value="dirichlet" selected="true">simple Dirichlet prior</option> 147 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
148 <option value="dmix">mixture of Dirichlets prior</option> 148 <option value="dmix">mixture of Dirichlets prior</option>
149 <option value="mega">extremely low variance dmix</option> 149 <option value="mega">extremely low variance dmix</option>
150 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option> 150 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
151 <option value="addone">add +1 to each observed count</option> 151 <option value="addone">add +1 to each observed count</option>
152 </param> 152 </param>
153 <when value="dirichlet"> 153 <when value="dirichlet">
154 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/> 154 <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
155 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 155 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
156 </when> 156 </when>
157 <when value="dmix"> 157 <when value="dmix">
158 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 158 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
159 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 159 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
160 </when> 160 </when>
161 <when value="mega"> 161 <when value="mega">
162 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 162 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
163 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 163 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
164 </when> 164 </when>
165 <when value="megap"> 165 <when value="megap">
166 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> 166 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
167 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> 167 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
168 </when> 168 </when>
169 <when value="addone" /> 169 <when value="addone"/>
170 </conditional> 170 </conditional>
171 <conditional name="spmap_type"> 171 <conditional name="spmap_type">
172 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap"> 172 <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
173 <option value="uni" selected="true">uni</option> 173 <option value="uni" selected="true">uni</option>
174 <option value="pam">pam</option> 174 <option value="pam">pam</option>
175 <option value="cons">Use starting point from string</option> 175 <option value="cons">Use starting point from string</option>
176 </param> 176 </param>
177 <when value="uni"> 177 <when value="uni">
178 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/> 178 <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
179 </when> 179 </when>
180 <when value="pam"> 180 <when value="pam">
181 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/> 181 <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
182 </when> 182 </when>
183 <when value="cons"> 183 <when value="cons">
184 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/> 184 <param argument="-cons" type="text" value="" label="Starting point from string"/>
185 </when> 185 </when>
186 </conditional> 186 </conditional>
187 </when> 187 </when>
188 </conditional> 188 </conditional>
189 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" /> 189 <param argument="-nmotifs" type="integer" value="1" label="Number of different motifs to search"/>
190 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/> 190 <param argument="-evt" type="float" value="inf" label="E-value to stop looking for motifs"/>
191 <conditional name="mod_type"> 191 <conditional name="mod_type">
192 <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod"> 192 <param name="mod_type_selector" argument="-mod" type="select" label="Expected motif distribution">
193 <option value="oops">One Occurrence Per Sequence</option> 193 <option value="oops">One Occurrence Per Sequence</option>
194 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option> 194 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
195 <option value="anr">Any Number of Repetitions</option> 195 <option value="anr">Any Number of Repetitions</option>
196 </param> 196 </param>
197 <when value="oops" /> 197 <when value="oops"/>
198 <when value="zoops"> 198 <when value="zoops">
199 <conditional name="motif_occurrence_type"> 199 <conditional name="motif_occurrence_type">
200 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences"> 200 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
201 <option value="default" selected="true">Use defaults</option> 201 <option value="default" selected="true">Use defaults</option>
202 <option value="nsites">nsites</option> 202 <option value="nsites">nsites</option>
203 <option value="min_max_sites">min and max sites</option> 203 <option value="min_max_sites">min and max sites</option>
204 </param> 204 </param>
205 <when value="default" /> 205 <when value="default"/>
206 <when value="nsites"> 206 <when value="nsites">
207 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/> 207 <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
208 </when> 208 </when>
209 <when value="min_max_sites"> 209 <when value="min_max_sites">
210 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/> 210 <param argument="-minsites" type="integer" value="1" label="minsites"/>
211 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/> 211 <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
212 </when> 212 </when>
213 </conditional> 213 </conditional>
214 </when> 214 </when>
215 <when value="anr"> 215 <when value="anr">
216 <conditional name="motif_occurrence_type"> 216 <conditional name="motif_occurrence_type">
217 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences"> 217 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
218 <option value="default" selected="true">Use defaults</option> 218 <option value="default" selected="true">Use defaults</option>
219 <option value="nsites">nsites</option> 219 <option value="nsites">nsites</option>
220 <option value="min_max_sites">min and max sites</option> 220 <option value="min_max_sites">min and max sites</option>
221 </param> 221 </param>
222 <when value="default" /> 222 <when value="default"/>
223 <when value="nsites"> 223 <when value="nsites">
224 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/> 224 <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
225 </when> 225 </when>
226 <when value="min_max_sites"> 226 <when value="min_max_sites">
227 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/> 227 <param argument="-minsites" type="integer" value="1" label="minsites"/>
228 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/> 228 <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
229 </when> 229 </when>
230 </conditional> 230 </conditional>
231 </when> 231 </when>
232 </conditional> 232 </conditional>
233 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/> 233 <param argument="-wnsites" type="float" value="0.8" label="Weight on the prior on nsites"/>
234 <conditional name="motif_width_type"> 234 <conditional name="motif_width_type">
235 <param name="motif_width_type_selector" type="select" label="Motif width type"> 235 <param name="motif_width_type_selector" type="select" label="Motif width type">
236 <option value="exact">Exact width</option> 236 <option value="exact">Exact width</option>
237 <option value="range" selected="true">Specify a range</option> 237 <option value="range" selected="true">Specify a range</option>
238 </param> 238 </param>
239 <when value="exact"> 239 <when value="exact">
240 <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/> 240 <param name="width" argument="-w" type="integer" value="10" label="Width of motif to search"/>
241 </when> 241 </when>
242 <when value="range"> 242 <when value="range">
243 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/> 243 <param argument="-minw" type="integer" value="8" label="Min width of motif to search"/>
244 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/> 244 <param argument="-maxw" type="integer" value="50" label="Max width of motif to search"/>
245 </when> 245 </when>
246 </conditional> 246 </conditional>
247 <conditional name="motif_trim_type"> 247 <conditional name="motif_trim_type">
248 <param name="motif_trim_type_selector" type="select" label="Motif trim type"> 248 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
249 <option value="nomatrim">No motif trim</option> 249 <option value="nomatrim">No motif trim</option>
250 <option value="trim" selected="true">Trim motif</option> 250 <option value="trim" selected="true">Trim motif</option>
251 </param> 251 </param>
252 <when value="nomatrim" /> 252 <when value="nomatrim"/>
253 <when value="trim"> 253 <when value="trim">
254 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/> 254 <param argument="-wg" type="integer" value="11" label="Gap cost"/>
255 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/> 255 <param argument="-ws" type="integer" value="1" label="Space cost"/>
256 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/> 256 <param argument="-noendgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False" label="Do not penalize endgaps"/>
257 </when> 257 </when>
258 </conditional> 258 </conditional>
259 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/> 259 <param argument="-bfile" type="data" format="txt" optional="True" label="Background Model"/>
260 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/> 260 <param name="pspfile" argument="-psp" type="data" format="txt" optional="True" label="Position-Specific Prior"/>
261 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/> 261 <param argument="-maxiter" type="integer" value="50" label="Number of iterations of EM to run"/>
262 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/> 262 <param argument="-distance" type="float" value="0.001" label="Convergence criterion"/>
263 <conditional name="branching_type"> 263 <conditional name="branching_type">
264 <param name="branching_type_selector" type="select" label="x-branching type"> 264 <param name="branching_type_selector" type="select" label="x-branching type">
265 <option value="x_branch">Perform x-branching</option> 265 <option value="x_branch">Perform x-branching</option>
266 <option value="no_x_branch" selected="true">No x-branching</option> 266 <option value="no_x_branch" selected="true">No x-branching</option>
267 </param> 267 </param>
268 <when value="no_x_branch" /> 268 <when value="no_x_branch"/>
269 <when value="x_branch"> 269 <when value="x_branch">
270 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/> 270 <param argument="-bfactor" type="integer" value="3" label="Number of iterations of branching"/>
271 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/> 271 <param argument="-heapsize" type="integer" value="64" label="Maximum number of heaps to use"/>
272 </when> 272 </when>
273 </conditional> 273 </conditional>
274 </when> 274 </when>
275 </conditional> 275 </conditional>
276 <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"> 276 <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
277 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 277 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
278 </param> 278 </param>
279 </inputs> 279 </inputs>
280 <outputs> 280 <outputs>
281 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> 281 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>