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comparison fimo.xml @ 13:4eb02864e5df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:00 -0400
parents c470b36b592d
children c1a9a297ba8b
comparison
equal deleted inserted replaced
12:02f6ad791bbf 13:4eb02864e5df
1 <tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0"> 1 <tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
2 <description>- Scan a set of sequences for motifs.</description> 2 <description>- Scan a set of sequences for motifs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p output && 8 fimo
9 python '$__tool_directory__/fimo_wrapper.py' 9 -o ./out/
10 --input_motifs '${input_motifs}' 10 $scanrc
11 #if str($fasta_type.fasta_type_selector) == 'history': 11 #if str( $options_type.options_type_selector ) == 'advanced':
12 --input_fasta '${fasta_type.input_database}' 12 --thresh $options_type.thresh
13 #else: 13 $options_type.qv_thresh
14 --input_fasta '${fasta_type.input_database.fields.path}' 14 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
15 #end if 15 --bgfile --motif--
16 --options_type $options_type.options_type_selector 16 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
17 #if str($options_type.options_type_selector) == 'advanced': 17 --bgfile $options_type.bgfile_type.bgfile
18 --alpha '${options_type.alpha}' 18 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
19 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': 19 --bgfile --uniform--
20 --bgfile 'motif-file' 20 #end if
21 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': 21 $options_type.max_strand
22 --bgfile '${options_type.bgfile_type.bgfile}' 22 --max-stored-scores $options_type.max_stored_scores
23
24 #if str( $options_type.motifs_cond.motif_selector) == 'yes':
25 #for $motif in $options_type.motifs_cond.motifs:
26 --motif $motif.motif
27 #end for
28 #end if
29
30 --motif-pseudo $options_type.motif_pseudo
31 $options_type.no_qvalue
32 $options_type.parse_genomic_coords
33
34 #if str( $options_type.psp_cond.psp_selector ) == 'yes':
35 --psp $options_type.psp_cond.input_psp
36 --alpha $options_type.psp_cond.alpha
37 #end if
38
39 #if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
40 --prior-dist $options_type.prior_dist_cond.input_prior_dist
41 #end if
23 #end if 42 #end if
24 ${options_type.max_strand} 43 '$input_motifs'
25 --max_stored_scores '${options_type.max_stored_scores}' 44 #if str($fasta_type.fasta_type_selector) == 'history':
26 #if str($options_type.motifs_cond.motifs_selector) == 'no': 45 '${fasta_type.input_database}'
27 #for $motif in $options_type.motifs: 46 #else:
28 --motif '${motif.motif}' 47 '${fasta_type.input_database.fields.path}'
29 #end for
30 #end if 48 #end if
31 --output_separate_motifs ${options_type.output_separate_motifs} 49 && mv ./out/fimo.html '${html_outfile}'
32 --motif_pseudo '${options_type.motif_pseudo}' 50 && mv ./out/fimo.txt '${txt_outfile}'
33 ${options_type.no_qvalue} 51 && mv ./out/fimo.xml '${xml_outfile}'
34 ${options_type.norc} 52 && mv ./out/fimo.gff '${gff_outfile}'
35 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
36 --parse_genomic_coord 'yes'
37 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
38 #end if
39 #if str($options_type.psp_cond.psp_selector) == 'yes':
40 --input_psp '${input_psp}'
41 #end if
42 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
43 --input_prior_dist '${input_prior_dist}'
44 #end if
45 ${options_type.qv_thresh}
46 --thresh ${options_type.thresh}
47 #end if
48 --output_path '${html_outfile.files_path}'
49 --html_output '${html_outfile}'
50 --interval_output '${interval_outfile}'
51 --txt_output '${txt_outfile}'
52 --xml_output '${xml_outfile}'
53 --gff_output '${gff_outfile}'
54 ]]></command> 53 ]]></command>
55 <inputs> 54 <inputs>
56 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/> 55 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file"
56 help="DREME or MEME output XML file containing found motifs"/>
57 <conditional name="fasta_type"> 57 <conditional name="fasta_type">
58 <param name="fasta_type_selector" type="select" label="Source for sequence to search"> 58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
59 <option value="cached">Locally Cached sequences</option> 59 <option value="cached">Locally Cached sequences</option>
60 <option value="history" selected="true">Sequences from your history</option> 60 <option value="history" selected="true">Sequences from your history</option>
61 </param> 61 </param>
66 </when> 66 </when>
67 <when value="history"> 67 <when value="history">
68 <param format="fasta" name="input_database" type="data" label="Sequences"/> 68 <param format="fasta" name="input_database" type="data" label="Sequences"/>
69 </when> 69 </when>
70 </conditional> 70 </conditional>
71 <param name="scanrc" label="Check reverse complement strand" type="boolean"
72 truevalue="" falsevalue="--norc" checked="False"
73 help="Search for motifs also on reverse complement strand"/>
71 <conditional name="options_type"> 74 <conditional name="options_type">
72 <param name="options_type_selector" type="select" label="Options configuration"> 75 <param name="options_type_selector" type="select" label="Options configuration">
73 <option value="basic" selected="true">Basic</option> 76 <option value="basic" selected="true">Basic</option>
74 <option value="advanced">Advanced</option> 77 <option value="advanced">Advanced</option>
75 </param> 78 </param>
76 <when value="basic" /> 79 <when value="basic"/>
77 <when value="advanced"> 80 <when value="advanced">
78 <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 <param name="thresh" type="float" value="1e-4" argument="--thresh"
82 label="Output threshold for displaying search results"
83 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."/>
84 <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
85 type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False"
86 help="Default: apply set threshold on p-values"/>
79 <conditional name="bgfile_type"> 87 <conditional name="bgfile_type">
80 <param name="bgfile_type_selector" type="select" label="Background file type"> 88 <param name="bgfile_type_selector" type="select" label="Background model selection">
81 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option> 89 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
82 <option value="motif_file">Use frequencies from motif file</option> 90 <option value="motif_file">Use 0-order letter frequencies from motif file</option>
83 <option value="bgfile">Use frequencies from background file</option> 91 <option value="bgfile">Use 0-order letter frequencies from background file</option>
92 <option value="uniform_distr">Use uniform letter frequencies</option>
84 </param> 93 </param>
85 <when value="motif_file" /> 94 <when value="motif_file" />
86 <when value="default" /> 95 <when value="default" />
96 <when value="uniform_distr" />
87 <when value="bgfile"> 97 <when value="bgfile">
88 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/> 98 <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)"/>
89 </when> 99 </when>
90 </conditional> 100 </conditional>
91 <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."/> 101 <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
92 <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" /> 102 type="boolean" truevalue="--max-strand" falsevalue="" checked="False"
103 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)."/>
104 <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
105 label="Maximum number of scores that will be stored"
106 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."/>
93 <conditional name="motifs_cond"> 107 <conditional name="motifs_cond">
94 <param name="motifs_selector" type="select" label="Use all motifs in input?"> 108 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
95 <option value="yes" selected="true">Yes</option>
96 <option value="no">No</option>
97 </param>
98 <when value="yes"/>
99 <when value="no">
100 <repeat name="motifs" title="Limit to specified motif">
101 <param name="motif" type="text" value="" label="Specify motif by id" />
102 </repeat>
103 </when>
104 </conditional>
105 <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">
106 <option value="no" selected="true">No</option>
107 <option value="yes">Yes</option>
108 </param>
109 <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"/>
110 <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)."/>
111 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
112 <conditional name="parse_genomic_coord_cond">
113 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
114 <option value="no" selected="true">No</option> 109 <option value="no" selected="true">No</option>
115 <option value="yes">Yes</option> 110 <option value="yes">Yes</option>
116 </param> 111 </param>
112 <when value="no"/>
117 <when value="yes"> 113 <when value="yes">
118 <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"> 114 <repeat name="motifs" title="Supply input motif ID">
119 <option value="no" selected="true">No</option> 115 <param name="motif" type="text" value="" label="Motif ID" />
120 <option value="yes">Yes</option> 116 </repeat>
121 </param> 117 </when>
122 </when> 118 </conditional>
123 <when value="no"/> 119 <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
124 </conditional> 120 label="Pseudocount to add to counts in motif matrix"
121 help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
122 <param name="no_qvalue" label="Disable q-value calculation?"
123 type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
124 help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
125 <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?"
126 type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
127 help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
125 <conditional name="psp_cond"> 128 <conditional name="psp_cond">
126 <param name="psp_selector" type="select" label="Use position-specific priors?"> 129 <param name="psp_selector" type="select" label="Use position-specific priors?">
127 <option value="no" selected="true">No</option> 130 <option value="no" selected="true">No</option>
128 <option value="yes">Yes</option> 131 <option value="yes">Yes</option>
129 </param> 132 </param>
130 <when value="no"/> 133 <when value="no"/>
131 <when value="yes"> 134 <when value="yes">
132 <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/> 135 <param name="input_psp" type="data" format="txt" argument="--psp"
136 label="Select file containing position-specific priors"
137 help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
138 <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
139 label="Alpha parameter for calculating position-specific priors"
140 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)"/>
133 </when> 141 </when>
134 </conditional> 142 </conditional>
135 <conditional name="prior_dist_cond"> 143 <conditional name="prior_dist_cond">
136 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?"> 144 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
137 <option value="no" selected="true">No</option> 145 <option value="no" selected="true">No</option>
138 <option value="yes">Yes</option> 146 <option value="yes">Yes</option>
139 </param> 147 </param>
140 <when value="no"/> 148 <when value="no"/>
141 <when value="yes"> 149 <when value="yes">
142 <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/> 150 <param name="input_prior_dist" type="data" format="txt" argument="--prior-dist"
143 </when> 151 label="Select dataset containing binned distribution of priors"
144 </conditional> 152 help="This file can be generated using the MEME suite tool create-priors"/>
145 <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."/> 153 </when>
146 <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."/> 154 </conditional>
147 </when> 155 </when>
148 </conditional> 156 </conditional>
149 <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"> 157 <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">
150 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 158 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
151 </param> 159 </param>
160 <section name="output_options" title="Additional output options">
161 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
162 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>
163 <param name="gff_outfile" type="boolean" value="False" label="Output GFF file" help="FIMO GFF output file"/>
164 </section>
152 </inputs> 165 </inputs>
153 <outputs> 166 <outputs>
167 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
168 <actions>
169 <conditional name="fasta_type.fasta_type_selector">
170 <when value="cached">
171 <action type="metadata" name="dbkey">
172 <option type="from_data_table" name="all_fasta" column="1" offset="0">
173 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
174 </option>
175 </action>
176 </when>
177 </conditional>
178 </actions>
179 </data>
154 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"> 180 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
181 <filter>(output_options['html_outfile'] is True)</filter>
155 <actions> 182 <actions>
156 <conditional name="fasta_type.fasta_type_selector"> 183 <conditional name="fasta_type.fasta_type_selector">
157 <when value="cached"> 184 <when value="cached">
158 <action type="metadata" name="dbkey"> 185 <action type="metadata" name="dbkey">
159 <option type="from_data_table" name="all_fasta" column="1" offset="0"> 186 <option type="from_data_table" name="all_fasta" column="1" offset="0">
163 </action> 190 </action>
164 </when> 191 </when>
165 </conditional> 192 </conditional>
166 </actions> 193 </actions>
167 </data> 194 </data>
168 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)"> 195 <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
196 <filter>(output_options['gff_outfile'] is True)</filter>
169 <actions> 197 <actions>
170 <conditional name="fasta_type.fasta_type_selector"> 198 <conditional name="fasta_type.fasta_type_selector">
171 <when value="cached"> 199 <when value="cached">
172 <action type="metadata" name="dbkey"> 200 <action type="metadata" name="dbkey">
173 <option type="from_data_table" name="all_fasta" column="1" offset="0"> 201 <option type="from_data_table" name="all_fasta" column="1" offset="0">
176 </action> 204 </action>
177 </when> 205 </when>
178 </conditional> 206 </conditional>
179 </actions> 207 </actions>
180 </data> 208 </data>
181 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)"> 209 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
182 <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter> 210 <filter>(output_options['xml_outfile'] is True)</filter>
183 <actions> 211 <actions>
184 <conditional name="fasta_type.fasta_type_selector"> 212 <conditional name="fasta_type.fasta_type_selector">
185 <when value="cached"> 213 <when value="cached">
186 <action type="metadata" name="dbkey"> 214 <action type="metadata" name="dbkey">
187 <option type="from_data_table" name="all_fasta" column="1" offset="0"> 215 <option type="from_data_table" name="all_fasta" column="1" offset="0">
190 </action> 218 </action>
191 </when> 219 </when>
192 </conditional> 220 </conditional>
193 </actions> 221 </actions>
194 </data> 222 </data>
195 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
196 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
197 <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
198 </collection>
199 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
200 <actions>
201 <conditional name="fasta_type.fasta_type_selector">
202 <when value="cached">
203 <action type="metadata" name="dbkey">
204 <option type="from_data_table" name="all_fasta" column="1" offset="0">
205 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
206 </option>
207 </action>
208 </when>
209 </conditional>
210 </actions>
211 </data>
212 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
213 <actions>
214 <conditional name="fasta_type.fasta_type_selector">
215 <when value="cached">
216 <action type="metadata" name="dbkey">
217 <option type="from_data_table" name="all_fasta" column="1" offset="0">
218 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
219 </option>
220 </action>
221 </when>
222 </conditional>
223 </actions>
224 </data>
225 </outputs> 223 </outputs>
226 <tests> 224 <tests>
227 <test> 225 <test expect_num_outputs="4">
228 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> 226 <param name="input_motifs" value="meme_fimo_input_1.xml" ftype="memexml"/>
229 <param name="fasta_type_selector" value="history"/> 227 <param name="fasta_type_selector" value="history"/>
230 <param name="input_database" value="phiX.fasta" ftype="fasta"/> 228 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
229 <param name="scanrc" value="true"/>
231 <param name="options_type_selector" value="basic"/> 230 <param name="options_type_selector" value="basic"/>
231 <param name="html_outfile" value="True"/>
232 <param name="xml_outfile" value="True"/>
233 <param name="gff_outfile" value="True"/>
232 <param name="non_commercial_use" value="True"/> 234 <param name="non_commercial_use" value="True"/>
233 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/> 235 <output name="html_outfile" file="fimo_output_test1.html" lines_diff="20"/>
234 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/> 236 <output name="txt_outfile" file="fimo_output_test1.txt"/>
235 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/> 237 <output name="xml_outfile" file="fimo_output_test1.xml" lines_diff="20"/>
236 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/> 238 <output name="gff_outfile" file="fimo_output_test1.gff"/>
237 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
238 </test> 239 </test>
239 <test> 240 <test expect_num_outputs="4">
240 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> 241 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
241 <param name="fasta_type_selector" value="history"/> 242 <param name="fasta_type_selector" value="history"/>
242 <param name="input_database" value="phiX.fasta" ftype="fasta"/> 243 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
244 <param name="scanrc" value="true"/>
243 <param name="options_type_selector" value="advanced"/> 245 <param name="options_type_selector" value="advanced"/>
246 <param name="bgfile_type_selector" value="bgfile"/>
247 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
248 <param name="html_outfile" value="True"/>
249 <param name="xml_outfile" value="True"/>
250 <param name="gff_outfile" value="True"/>
244 <param name="non_commercial_use" value="True"/> 251 <param name="non_commercial_use" value="True"/>
245 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> 252 <output name="html_outfile" file="fimo_output_test2.html" lines_diff="20"/>
246 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> 253 <output name="txt_outfile" file="fimo_output_test2.txt"/>
247 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/> 254 <output name="xml_outfile" file="fimo_output_test2.xml" lines_diff="20"/>
248 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/> 255 <output name="gff_outfile" file="fimo_output_test2.gff"/>
249 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
250 </test> 256 </test>
251 <test> 257 <test expect_num_outputs="3">
252 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> 258 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
253 <param name="fasta_type_selector" value="history"/> 259 <param name="fasta_type_selector" value="history"/>
254 <param name="input_database" value="phiX.fasta" ftype="fasta"/> 260 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
261 <param name="scanrc" value="true"/>
255 <param name="options_type_selector" value="advanced"/> 262 <param name="options_type_selector" value="advanced"/>
256 <param name="parse_genomic_coord" value="yes"/> 263 <param name="thresh" value="0.01"/>
257 <param name="remove_duplicate_coords" value="yes"/> 264 <param name="bgfile_type_selector" value="uniform_distr"/>
258 <param name="output_separate_motifs" value="yes"/> 265 <param name="motif_selector" value="yes"/>
266 <repeat name="motifs">
267 <param name="motif" value="ACTAAYH"/>
268 </repeat>
269 <param name="html_outfile" value="True"/>
270 <param name="xml_outfile" value="True"/>
271 <param name="gff_outfile" value="False"/>
259 <param name="non_commercial_use" value="True"/> 272 <param name="non_commercial_use" value="True"/>
260 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> 273 <output name="html_outfile" file="fimo_output_test3.html" lines_diff="20"/>
261 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> 274 <output name="txt_outfile" file="fimo_output_test3.txt"/>
262 <output_collection name="motifs" type="list"> 275 <output name="xml_outfile" file="fimo_output_test3.xml" lines_diff="20"/>
263 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
264 </output_collection>
265 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
266 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
267 </test> 276 </test>
268 </tests> 277 </tests>
269 <help> 278 <help>
270 279
271 .. class:: warningmark 280 .. class:: warningmark