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comparison fimo.xml @ 1:c9623dbfb799 draft

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author devteam
date Fri, 01 Dec 2017 10:22:02 -0500
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0:a479851ea251 1:c9623dbfb799
1 <tool id="meme_fimo" name="FIMO" version="0.0.1">
2 <requirements><requirement type="package">meme</requirement></requirements>
3 <description>- Find Individual Motif Occurrences</description>
4 <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
5
6 #if str( $options_type.options_type_selector ) == 'advanced':
7 --max-seq-length "${options_type.max_seq_length}"
8 --max-stored-scores "${options_type.max_stored_scores }"
9 --motif-pseudo "${options_type.motif_pseudo}"
10 ${options_type.norc}
11 --output-pthresh "${options_type.output_pthresh}"
12
13
14 #for $motif in $options_type.motifs:
15 --motif "${motif.motif}"
16 #end for
17
18 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
19 --bgfile "motif-file"
20 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
21 --bgfile "${options_type.bgfile_type.bgfile}"
22 #end if
23
24 #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
25 --no-qvalue
26 #else:
27 --output-qthresh "${options_type.qvalue_type.output_qthresh}"
28 #end if
29 #end if
30
31 "${input_motifs}"
32
33 #if str( $fasta_type.fasta_type_selector ) == 'history':
34 "${fasta_type.input_database}"
35 #else:
36 "${fasta_type.input_database.fields.path}"
37 #end if
38
39 '
40
41 '${html_outfile.files_path}'
42
43 '${html_outfile}'
44
45 '${interval_outfile}'
46
47 '${txt_outfile}'
48
49 '${xml_outfile}'
50
51 '${gff_outfile}'
52
53 </command>
54 <inputs>
55 <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
56
57 <conditional name="fasta_type">
58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
59 <option value="cached">Locally Cached sequences</option>
60 <option value="history" selected="true">Sequences from your history</option>
61 </param>
62 <when value="cached">
63 <param name="input_database" type="select" label="Genome to search">
64 <options from_data_table="all_fasta">
65 </options>
66 </param>
67 </when>
68 <when value="history">
69 <param format="fasta" name="input_database" type="data" label="Sequences"/>
70 </when>
71 </conditional>
72
73 <conditional name="options_type">
74 <param name="options_type_selector" type="select" label="Options Configuration">
75 <option value="basic" selected="true">Basic</option>
76 <option value="advanced">Advanced</option>
77 </param>
78 <when value="basic">
79 <!-- do nothing here -->
80 </when>
81 <when value="advanced">
82
83 <conditional name="bgfile_type">
84 <param name="bgfile_type_selector" type="select" label="Background file type">
85 <option value="motif-file">Use Frequencies from Motif File</option>
86 <option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
87 <option value="bgfile">Use Frequencies from Background File</option>
88 </param>
89 <when value="motif-file">
90 <!-- do nothing here -->
91 </when>
92 <when value="default">
93 <!-- do nothing here -->
94 </when>
95 <when value="bgfile">
96 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
97 </when>
98 </conditional>
99
100 <repeat name="motifs" title="Limit to specified motif">
101 <param name="motif" type="text" value="" label="Specify motif by id" />
102 </repeat>
103
104 <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
105 <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
106 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
107 <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
108 <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
109
110 <conditional name="qvalue_type">
111 <param name="qvalue_type_selector" type="select" label="q-value options">
112 <option value="no-qvalue">Do not compute q-value</option>
113 <option value="q-value" selected="true">Compute q-value</option>
114 </param>
115 <when value="no-qvalue">
116 <!-- do nothing here -->
117 </when>
118 <when value="q-value">
119 <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
120 </when>
121 </conditional>
122
123 </when>
124 </conditional>
125
126 <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">
127 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
128 </param>
129
130 </inputs>
131 <outputs>
132 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
133 <actions>
134 <conditional name="fasta_type.fasta_type_selector">
135 <when value="cached">
136 <action type="metadata" name="dbkey">
137 <option type="from_data_table" name="all_fasta" column="1" offset="0">
138 <filter type="param_value" column="0" value="seq" keep="True"/>
139 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
140 </option>
141 </action>
142 </when>
143 </conditional>
144 </actions>
145 </data>
146 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
147 <actions>
148 <conditional name="fasta_type.fasta_type_selector">
149 <when value="cached">
150 <action type="metadata" name="dbkey">
151 <option type="from_data_table" name="all_fasta" column="1" offset="0">
152 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
153 </option>
154 </action>
155 </when>
156 </conditional>
157 </actions>
158 </data>
159 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
160 <actions>
161 <conditional name="fasta_type.fasta_type_selector">
162 <when value="cached">
163 <action type="metadata" name="dbkey">
164 <option type="from_data_table" name="all_fasta" column="1" offset="0">
165 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
166 </option>
167 </action>
168 </when>
169 </conditional>
170 </actions>
171 </data>
172 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
173 <actions>
174 <conditional name="fasta_type.fasta_type_selector">
175 <when value="cached">
176 <action type="metadata" name="dbkey">
177 <option type="from_data_table" name="all_fasta" column="1" offset="0">
178 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
179 </option>
180 </action>
181 </when>
182 </conditional>
183 </actions>
184 </data>
185 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
186 <actions>
187 <conditional name="fasta_type.fasta_type_selector">
188 <when value="cached">
189 <action type="metadata" name="dbkey">
190 <option type="from_data_table" name="all_fasta" column="1" offset="0">
191 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
192 </option>
193 </action>
194 </when>
195 </conditional>
196 </actions>
197 </data>
198 </outputs>
199 <tests>
200 <test>
201 <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
202 <param name="fasta_type_selector" value="history"/>
203 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
204 <param name="options_type_selector" value="basic"/>
205 <param name="non_commercial_use" value="True"/>
206 <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
207 <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
208 <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
209 <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
210 <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
211 </test>
212 </tests>
213 <help>
214
215 .. class:: warningmark
216
217 **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.**
218
219 .. class:: infomark
220
221 **To cite FIMO:**
222 `Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21330290&gt;`_
223
224
225 For detailed information on FIMO, click here_. To view the license_.
226
227 ------
228
229 **Citation**
230
231 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
232
233
234 .. _here: http://meme.nbcr.net/meme/fimo-intro.html
235 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
236
237 </help>
238 </tool>