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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 10:19:40 +0000
parents c5209f38700d
children
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18:c5209f38700d 19:01f5d04846c4
1 <tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Scan a set of sequences for motifs</description> 2 <description>- Scan a set of sequences for motifs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">meme_fimo</xref> 7 <xref type="bio.tools">meme_fimo</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 fimo 12 fimo
13 -o ./out/ 13 -o ./out/
14 $scanrc 14 $scanrc
54 && mv ./out/fimo.tsv '${txt_outfile}' 54 && mv ./out/fimo.tsv '${txt_outfile}'
55 && mv ./out/fimo.xml '${xml_outfile}' 55 && mv ./out/fimo.xml '${xml_outfile}'
56 && mv ./out/fimo.gff '${gff_outfile}' 56 && mv ./out/fimo.gff '${gff_outfile}'
57 ]]></command> 57 ]]></command>
58 <inputs> 58 <inputs>
59 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" 59 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" help="DREME or MEME output XML file containing found motifs"/>
60 help="DREME or MEME output XML file containing found motifs"/>
61 <conditional name="fasta_type"> 60 <conditional name="fasta_type">
62 <param name="fasta_type_selector" type="select" label="Source for sequence to search"> 61 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
63 <option value="cached">Locally Cached sequences</option> 62 <option value="cached">Locally Cached sequences</option>
64 <option value="history" selected="true">Sequences from your history</option> 63 <option value="history" selected="true">Sequences from your history</option>
65 </param> 64 </param>
66 <when value="cached"> 65 <when value="cached">
67 <param name="input_database" type="select" label="Genome to search"> 66 <param name="input_database" type="select" label="Genome to search">
68 <options from_data_table="all_fasta" /> 67 <options from_data_table="all_fasta"/>
69 </param> 68 </param>
70 </when> 69 </when>
71 <when value="history"> 70 <when value="history">
72 <param format="fasta" name="input_database" type="data" label="Sequences"/> 71 <param name="input_database" type="data" format="fasta" label="Sequences"/>
73 </when> 72 </when>
74 </conditional> 73 </conditional>
75 <param name="scanrc" label="Check reverse complement strand" type="boolean" 74 <param name="scanrc" type="boolean" truevalue="" falsevalue="--norc" checked="False" label="Check reverse complement strand" help="Search for motifs also on reverse complement strand"/>
76 truevalue="" falsevalue="--norc" checked="False"
77 help="Search for motifs also on reverse complement strand"/>
78 <conditional name="options_type"> 75 <conditional name="options_type">
79 <param name="options_type_selector" type="select" label="Options configuration"> 76 <param name="options_type_selector" type="select" label="Options configuration">
80 <option value="basic" selected="true">Basic</option> 77 <option value="basic" selected="true">Basic</option>
81 <option value="advanced">Advanced</option> 78 <option value="advanced">Advanced</option>
82 </param> 79 </param>
83 <when value="basic"/> 80 <when value="basic"/>
84 <when value="advanced"> 81 <when value="advanced">
85 <param name="thresh" type="float" value="1e-4" argument="--thresh" 82 <param argument="--thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
86 label="Output threshold for displaying search results" 83 <param argument="--qv-thresh" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" label="Apply output threshold to q-values?" help="Default: apply set threshold on p-values"/>
87 help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
88 <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
89 type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False"
90 help="Default: apply set threshold on p-values"/>
91 <conditional name="bgfile_type"> 84 <conditional name="bgfile_type">
92 <param name="bgfile_type_selector" type="select" label="Background model selection"> 85 <param name="bgfile_type_selector" type="select" label="Background model selection">
93 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option> 86 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
94 <option value="motif_file">Use 0-order letter frequencies from motif file</option> 87 <option value="motif_file">Use 0-order letter frequencies from motif file</option>
95 <option value="bgfile">Use 0-order letter frequencies from background file</option> 88 <option value="bgfile">Use 0-order letter frequencies from background file</option>
96 <option value="uniform_distr">Use uniform letter frequencies</option> 89 <option value="uniform_distr">Use uniform letter frequencies</option>
97 </param> 90 </param>
98 <when value="motif_file" /> 91 <when value="motif_file"/>
99 <when value="default" /> 92 <when value="default"/>
100 <when value="uniform_distr" /> 93 <when value="uniform_distr"/>
101 <when value="bgfile"> 94 <when value="bgfile">
102 <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/> 95 <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
103 </when> 96 </when>
104 </conditional> 97 </conditional>
105 <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand" 98 <param argument="--max-strand" type="boolean" truevalue="--max-strand" falsevalue="" checked="False" label="Report best match in case of overlapping matches on both strands?" help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
106 type="boolean" truevalue="--max-strand" falsevalue="" checked="False" 99 <param argument="--max-stored-scores" type="integer" value="100000" label="Maximum number of scores that will be stored" help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
107 help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
108 <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
109 label="Maximum number of scores that will be stored"
110 help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
111 <conditional name="motifs_cond"> 100 <conditional name="motifs_cond">
112 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?"> 101 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
113 <option value="no" selected="true">No</option> 102 <option value="no" selected="true">No</option>
114 <option value="yes">Yes</option> 103 <option value="yes">Yes</option>
115 </param> 104 </param>
116 <when value="no"/> 105 <when value="no"/>
117 <when value="yes"> 106 <when value="yes">
118 <repeat name="motifs" title="Supply input motif ID"> 107 <repeat name="motifs" title="Supply input motif ID">
119 <param name="motif" type="text" value="" label="Specify motif by id"> 108 <param name="motif" type="text" value="" label="Specify motif by id">
120 <validator type="empty_field" /> 109 <validator type="empty_field"/>
121 <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator> 110 <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator>
122 </param> 111 </param>
123 </repeat> 112 </repeat>
124 </when> 113 </when>
125 </conditional> 114 </conditional>
126 <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo" 115 <param argument="--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"/>
127 label="Pseudocount to add to counts in motif matrix" 116 <param argument="--no-qvalue" type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" label="Disable q-value calculation?" help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
128 help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/> 117 <param name="parse_genomic_coords" argument="--parse-genomic-coord" type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" label="Check each sequence header for UCSC-style genomic coordinates?" help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
129 <param name="no_qvalue" label="Disable q-value calculation?"
130 type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
131 help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
132 <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?"
133 type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
134 help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
135 <conditional name="psp_cond"> 118 <conditional name="psp_cond">
136 <param name="psp_selector" type="select" label="Use position-specific priors?"> 119 <param name="psp_selector" type="select" label="Use position-specific priors?">
137 <option value="no" selected="true">No</option> 120 <option value="no" selected="true">No</option>
138 <option value="yes">Yes</option> 121 <option value="yes">Yes</option>
139 </param> 122 </param>
140 <when value="no"/> 123 <when value="no"/>
141 <when value="yes"> 124 <when value="yes">
142 <param name="input_psp" type="data" format="txt" argument="--psp" 125 <param name="input_psp" argument="--psp" type="data" format="txt" label="Select file containing position-specific priors" help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
143 label="Select file containing position-specific priors" 126 <param argument="--alpha" type="float" min="0" max="1.0" value="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)"/>
144 help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
145 <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
146 label="Alpha parameter for calculating position-specific priors"
147 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)"/>
148 </when> 127 </when>
149 </conditional> 128 </conditional>
150 <conditional name="prior_dist_cond"> 129 <conditional name="prior_dist_cond">
151 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?"> 130 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
152 <option value="no" selected="true">No</option> 131 <option value="no" selected="true">No</option>
153 <option value="yes">Yes</option> 132 <option value="yes">Yes</option>
154 </param> 133 </param>
155 <when value="no"/> 134 <when value="no"/>
156 <when value="yes"> 135 <when value="yes">
157 <param name="input_prior_dist" type="data" format="txt" argument="--prior-dist" 136 <param name="input_prior_dist" argument="--prior-dist" type="data" format="txt" label="Select dataset containing binned distribution of priors" help="This file can be generated using the MEME suite tool create-priors"/>
158 label="Select dataset containing binned distribution of priors"
159 help="This file can be generated using the MEME suite tool create-priors"/>
160 </when> 137 </when>
161 </conditional> 138 </conditional>
162 </when> 139 </when>
163 </conditional> 140 </conditional>
164 <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"> 141 <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.">
165 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 142 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
166 </param> 143 </param>
167 <section name="output_options" title="Additional output options"> 144 <section name="output_options" title="Additional output options">
168 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/> 145 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
169 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/> 146 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>
197 </action> 174 </action>
198 </when> 175 </when>
199 </conditional> 176 </conditional>
200 </actions> 177 </actions>
201 </data> 178 </data>
202 <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)"> 179 <data format="gff" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
203 <filter>(output_options['gff_outfile'] is True)</filter> 180 <filter>(output_options['gff_outfile'] is True)</filter>
204 <actions> 181 <actions>
205 <conditional name="fasta_type.fasta_type_selector"> 182 <conditional name="fasta_type.fasta_type_selector">
206 <when value="cached"> 183 <when value="cached">
207 <action type="metadata" name="dbkey"> 184 <action type="metadata" name="dbkey">
237 <param name="options_type_selector" value="basic"/> 214 <param name="options_type_selector" value="basic"/>
238 <param name="html_outfile" value="True"/> 215 <param name="html_outfile" value="True"/>
239 <param name="xml_outfile" value="True"/> 216 <param name="xml_outfile" value="True"/>
240 <param name="gff_outfile" value="True"/> 217 <param name="gff_outfile" value="True"/>
241 <param name="non_commercial_use" value="True"/> 218 <param name="non_commercial_use" value="True"/>
242 <output name="html_outfile" file="fimo_output_test1.html" compare="contains"/> 219 <output name="html_outfile" ftype="html">
243 <output name="txt_outfile" file="fimo_output_test1.txt" compare="contains"/> 220 <assert_contents>
244 <output name="xml_outfile" file="fimo_output_test1.xml" compare="contains"/> 221 <has_text text="TACTAAYM"/>
245 <output name="gff_outfile" file="fimo_output_test1.gff" compare="contains"/> 222 <has_text text="MEME file name"/>
223 </assert_contents>
224 </output>
225 <output name="txt_outfile">
226 <assert_contents>
227 <has_text text="motif_id"/>
228 <has_text text="sequence_name"/>
229 <has_text text="matched_sequence"/>
230 <has_text text="TACTAATA"/>
231 </assert_contents>
232 </output>
233 <output name="xml_outfile" ftype="memexml">
234 <assert_contents>
235 <has_text text="sequence-data num-sequences"/>
236 <has_text text="16569"/>
237 <has_text text="Cytosine"/>
238 <has_text text="TACTAACA"/>
239 </assert_contents>
240 </output>
241 <output name="gff_outfile" ftype="gff">
242 <assert_contents>
243 <has_text text="gff-version 3"/>
244 <has_text text="TACTAAYM_chrM"/>
245 <has_text text="qvalue"/>
246 <has_text text="nucleotide_motif"/>
247 <has_text text="fimo"/>
248 <has_text text="chrM"/>
249 <has_n_lines n="12"/>
250 </assert_contents>
251 </output>
246 </test> 252 </test>
247 <test expect_num_outputs="4"> 253 <test expect_num_outputs="4">
248 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> 254 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
249 <param name="fasta_type_selector" value="history"/> 255 <param name="fasta_type_selector" value="history"/>
250 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/> 256 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
254 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/> 260 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
255 <param name="html_outfile" value="True"/> 261 <param name="html_outfile" value="True"/>
256 <param name="xml_outfile" value="True"/> 262 <param name="xml_outfile" value="True"/>
257 <param name="gff_outfile" value="True"/> 263 <param name="gff_outfile" value="True"/>
258 <param name="non_commercial_use" value="True"/> 264 <param name="non_commercial_use" value="True"/>
259 <output name="html_outfile" file="fimo_output_test2.html" compare="contains"/> 265 <output name="html_outfile">
260 <output name="txt_outfile" file="fimo_output_test2.txt" compare="contains"/> 266 <assert_contents>
261 <output name="xml_outfile" file="fimo_output_test2.xml" compare="contains"/> 267 <has_text text="MOTIF"/>
262 <output name="gff_outfile" file="fimo_output_test2.gff" compare="contains"/> 268 <has_text text="WIDTH"/>
269 <has_text text="TTAACA"/>
270 <has_text text="GAATGT"/>
271 </assert_contents>
272 </output>
273 <output name="txt_outfile">
274 <assert_contents>
275 <has_text text="sequence_name"/>
276 <has_text text="motif_id"/>
277 <has_text text="matched_sequence"/>
278 <has_text text="ACTAAYH"/>
279 <has_text text="chrM"/>
280 </assert_contents>
281 </output>
282 <output name="xml_outfile" ftype="memexml">
283 <assert_contents>
284 <has_text text="MEME file name"/>
285 <has_text text="pseudocount"/>
286 <has_text text="Not G"/>
287 <has_text text="Keto"/>
288 </assert_contents>
289 </output>
290 <output name="gff_outfile" ftype="gff">
291 <assert_contents>
292 <has_text text="gff-version 3"/>
293 <has_text text="ID=ACTAAYH-DREME-1-4-chrM"/>
294 <has_text text="nucleotide_motif"/>
295 <has_text text="fimo"/>
296 <has_text text="chrM"/>
297 <has_n_lines n="12"/>
298 </assert_contents>
299 </output>
263 </test> 300 </test>
264 <test expect_num_outputs="3"> 301 <test expect_num_outputs="3">
265 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> 302 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
266 <param name="fasta_type_selector" value="history"/> 303 <param name="fasta_type_selector" value="history"/>
267 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/> 304 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
275 </repeat> 312 </repeat>
276 <param name="html_outfile" value="True"/> 313 <param name="html_outfile" value="True"/>
277 <param name="xml_outfile" value="True"/> 314 <param name="xml_outfile" value="True"/>
278 <param name="gff_outfile" value="False"/> 315 <param name="gff_outfile" value="False"/>
279 <param name="non_commercial_use" value="True"/> 316 <param name="non_commercial_use" value="True"/>
280 <output name="html_outfile" file="fimo_output_test3.html" compare="contains"/> 317 <output name="html_outfile">
281 <output name="txt_outfile" file="fimo_output_test3.txt" compare="contains"/> 318 <assert_contents>
282 <output name="xml_outfile" file="fimo_output_test3.xml" compare="contains"/> 319 <has_text text="top_buttons"/>
320 <has_text text="database_and_motifs"/>
321 <has_text text="YTAACA"/>
322 <has_text text="ACTAAYH"/>
323 <has_text text="DREME"/>
324 </assert_contents>
325 </output>
326 <output name="txt_outfile">
327 <assert_contents>
328 <has_text text="motif_alt_id"/>
329 <has_text text="matched_sequence"/>
330 <has_text text="ACTAAYH"/>
331 <has_text text="ACTAACA"/>
332 </assert_contents>
333 </output>
334 <output name="xml_outfile" ftype="memexml">
335 <assert_contents>
336 <has_text text="complement"/>
337 <has_text text="letter"/>
338 <has_text text="16569"/>
339 <has_text text="dna"/>
340 <has_text text="ACTAAYH"/>
341 </assert_contents>
342 </output>
283 </test> 343 </test>
284 </tests> 344 </tests>
285 <help> 345 <help>
286 346
287 .. class:: warningmark 347 .. class:: warningmark