Mercurial > repos > xuebing > sharplabtool
comparison tools/meme/fimo.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="meme_fimo" name="FIMO" version="0.0.1"> | |
2 <description>- Find Individual Motif Occurrences</description> | |
3 <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1" | |
4 | |
5 #if str( $options_type.options_type_selector ) == 'advanced': | |
6 --max-seq-length "${options_type.max_seq_length}" | |
7 --max-stored-scores "${options_type.max_stored_scores }" | |
8 --motif-pseudo "${options_type.motif_pseudo}" | |
9 ${options_type.norc} | |
10 --output-pthresh "${options_type.output_pthresh}" | |
11 | |
12 | |
13 #for $motif in $options_type.motifs: | |
14 --motif "${motif.motif}" | |
15 #end for | |
16 | |
17 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file': | |
18 --bgfile "motif-file" | |
19 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file': | |
20 --bgfile "${options_type.bgfile_type.bgfile}" | |
21 #end if | |
22 | |
23 #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue': | |
24 --no-qvalue | |
25 #else: | |
26 --output-qthresh "${options_type.qvalue_type.output_qthresh}" | |
27 #end if | |
28 #end if | |
29 | |
30 "${input_motifs}" | |
31 | |
32 #if str( $fasta_type.fasta_type_selector ) == 'history': | |
33 "${fasta_type.input_database}" | |
34 #else: | |
35 "${ filter( lambda x: str( x[0] ) == str( $fasta_type.input_database ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][3] }" | |
36 #end if | |
37 | |
38 ' | |
39 | |
40 '${html_outfile.files_path}' | |
41 | |
42 '${html_outfile}' | |
43 | |
44 '${interval_outfile}' | |
45 | |
46 '${txt_outfile}' | |
47 | |
48 '${xml_outfile}' | |
49 | |
50 '${gff_outfile}' | |
51 | |
52 </command> | |
53 <inputs> | |
54 <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/> | |
55 | |
56 <conditional name="fasta_type"> | |
57 <param name="fasta_type_selector" type="select" label="Source for sequence to search"> | |
58 <option value="cached">Locally Cached sequences</option> | |
59 <option value="history" selected="true">Sequences from your history</option> | |
60 </param> | |
61 <when value="cached"> | |
62 <param name="input_database" type="select" label="Genome to search"> | |
63 <options from_data_table="all_fasta"> | |
64 </options> | |
65 </param> | |
66 </when> | |
67 <when value="history"> | |
68 <param format="fasta" name="input_database" type="data" label="Sequences"/> | |
69 </when> | |
70 </conditional> | |
71 | |
72 <conditional name="options_type"> | |
73 <param name="options_type_selector" type="select" label="Options Configuration"> | |
74 <option value="basic" selected="true">Basic</option> | |
75 <option value="advanced">Advanced</option> | |
76 </param> | |
77 <when value="basic"> | |
78 <!-- do nothing here --> | |
79 </when> | |
80 <when value="advanced"> | |
81 | |
82 <conditional name="bgfile_type"> | |
83 <param name="bgfile_type_selector" type="select" label="Background file type"> | |
84 <option value="motif-file">Use Frequencies from Motif File</option> | |
85 <option value="default" selected="true">Use frequencies from non-redundant database (default)</option> | |
86 <option value="bgfile">Use Frequencies from Background File</option> | |
87 </param> | |
88 <when value="motif-file"> | |
89 <!-- do nothing here --> | |
90 </when> | |
91 <when value="default"> | |
92 <!-- do nothing here --> | |
93 </when> | |
94 <when value="bgfile"> | |
95 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" /> | |
96 </when> | |
97 </conditional> | |
98 | |
99 <repeat name="motifs" title="Limit to specified motif"> | |
100 <param name="motif" type="text" value="" label="Specify motif by id" /> | |
101 </repeat> | |
102 | |
103 <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" /> | |
104 <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" /> | |
105 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" /> | |
106 <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/> | |
107 <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" /> | |
108 | |
109 <conditional name="qvalue_type"> | |
110 <param name="qvalue_type_selector" type="select" label="q-value options"> | |
111 <option value="no-qvalue">Do not compute q-value</option> | |
112 <option value="q-value" selected="true">Compute q-value</option> | |
113 </param> | |
114 <when value="no-qvalue"> | |
115 <!-- do nothing here --> | |
116 </when> | |
117 <when value="q-value"> | |
118 <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" /> | |
119 </when> | |
120 </conditional> | |
121 | |
122 </when> | |
123 </conditional> | |
124 | |
125 <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"> | |
126 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> | |
127 </param> | |
128 | |
129 </inputs> | |
130 <outputs> | |
131 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"> | |
132 <actions> | |
133 <conditional name="fasta_type.fasta_type_selector"> | |
134 <when value="cached"> | |
135 <action type="metadata" name="dbkey"> | |
136 <option type="from_data_table" name="all_fasta" column="1" offset="0"> | |
137 <filter type="param_value" column="0" value="seq" keep="True"/> | |
138 <filter type="param_value" ref="fasta_type.input_database" column="1"/> | |
139 </option> | |
140 </action> | |
141 </when> | |
142 </conditional> | |
143 </actions> | |
144 </data> | |
145 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)"> | |
146 <actions> | |
147 <conditional name="fasta_type.fasta_type_selector"> | |
148 <when value="cached"> | |
149 <action type="metadata" name="dbkey"> | |
150 <option type="from_data_table" name="all_fasta" column="1" offset="0"> | |
151 <filter type="param_value" ref="fasta_type.input_database" column="0"/> | |
152 </option> | |
153 </action> | |
154 </when> | |
155 </conditional> | |
156 </actions> | |
157 </data> | |
158 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)"> | |
159 <actions> | |
160 <conditional name="fasta_type.fasta_type_selector"> | |
161 <when value="cached"> | |
162 <action type="metadata" name="dbkey"> | |
163 <option type="from_data_table" name="all_fasta" column="1" offset="0"> | |
164 <filter type="param_value" ref="fasta_type.input_database" column="0"/> | |
165 </option> | |
166 </action> | |
167 </when> | |
168 </conditional> | |
169 </actions> | |
170 </data> | |
171 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"> | |
172 <actions> | |
173 <conditional name="fasta_type.fasta_type_selector"> | |
174 <when value="cached"> | |
175 <action type="metadata" name="dbkey"> | |
176 <option type="from_data_table" name="all_fasta" column="1" offset="0"> | |
177 <filter type="param_value" ref="fasta_type.input_database" column="0"/> | |
178 </option> | |
179 </action> | |
180 </when> | |
181 </conditional> | |
182 </actions> | |
183 </data> | |
184 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)"> | |
185 <actions> | |
186 <conditional name="fasta_type.fasta_type_selector"> | |
187 <when value="cached"> | |
188 <action type="metadata" name="dbkey"> | |
189 <option type="from_data_table" name="all_fasta" column="1" offset="0"> | |
190 <filter type="param_value" ref="fasta_type.input_database" column="0"/> | |
191 </option> | |
192 </action> | |
193 </when> | |
194 </conditional> | |
195 </actions> | |
196 </data> | |
197 </outputs> | |
198 <tests> | |
199 <test> | |
200 <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/> | |
201 <param name="fasta_type_selector" value="history"/> | |
202 <param name="input_database" value="phiX.fasta" ftype="fasta"/> | |
203 <param name="options_type_selector" value="basic"/> | |
204 <param name="non_commercial_use" value="True"/> | |
205 <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/> | |
206 <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/> | |
207 <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/> | |
208 <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/> | |
209 <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/> | |
210 </test> | |
211 </tests> | |
212 <help> | |
213 | |
214 .. class:: warningmark | |
215 | |
216 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.** | |
217 | |
218 .. class:: infomark | |
219 | |
220 **To cite FIMO:** | |
221 `Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. <http://www.ncbi.nlm.nih.gov/pubmed/21330290>`_ | |
222 | |
223 | |
224 For detailed information on FIMO, click here_. To view the license_. | |
225 | |
226 .. _here: http://meme.nbcr.net/meme/fimo-intro.html | |
227 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html | |
228 | |
229 </help> | |
230 </tool> |