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comparison meme_chip.xml @ 0:fd58302909b8 draft

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author iuc
date Wed, 14 Mar 2018 11:15:15 -0400
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1 <tool id="meme_chip" name="MEME-ChIP" version="4.12.0">
2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #set options_type = $options_type_cond.options_type
9 meme-chip $input
10 -noecho
11 -db $meme_motif_databases.fields.path
12 #if $sequence_alphabet == 'dna':
13 -dna
14 #else:
15 -rna
16 -norc
17 #end if
18 -o '$output.files_path'
19
20 #if str($options_type)=='advanced':
21 -order $options_type_cond.background_model_order
22 #if str($options_type_cond.subsampling) == "no":
23 -norand
24 #end if
25 #if str($options_type_cond.subsampling_cond.subsampling) != "yes":
26 #set seed = $options_type_cond.subsampling_cond.subsampling.seed
27 #if str($seed) != "0":
28 -seed $options_type_cond.subsampling_cond.subsampling.seed
29 #end if
30 #end if
31 #if str($options_type_cond.nmeme) != "0":
32 -nmeme $options_type_cond.nmeme
33 #end if
34 #if str($options_type_cond.ccut) != "0":
35 -ccut $options_type_cond.ccut
36 #end if
37 -group-thresh $options_type_cond.group_threash
38 #if str($options_type_cond.group_weak) != "0":
39 -group-weak $options_type_cond.group_weak
40 #end if
41 -filter-thresh $options_type_cond.filter_threash
42 -meme-mod $options_type_cond.meme_mod
43 #if str($options_type_cond.meme_minw) != "0":
44 -meme-minw $options_type_cond.meme_minw
45 #end if
46 #if str($options_type_cond.meme_maxw) != "0":
47 -meme-maxw $options_type_cond.meme_maxw
48 #end if
49 #if str($options_type_cond.meme_nmotifs) != '0':
50 -meme-nmotifs $options_type_cond.meme_nmotifs
51 #end if
52 #if str($options_type_cond.meme_minsites) != "0":
53 -meme-minsites $options_type_cond.meme_minsites
54 #end if
55 #if str($options_type_cond.meme_maxsites) != "0":
56 -meme-maxsites $options_type_cond.meme_maxsites
57 #end if
58 #if str($options_type_cond.meme_pal) == "true":
59 -meme-pal
60 #end if
61 -dreme-e $options_type_cond.dreme_e
62 -dreme-m $options_type_cond.dreme_m
63 #if str($options_type_cond.centrimo_local) == "true":
64 -centrimo-local
65 #end if
66 #if str($options_type_cond.centrimo_score) != "0":
67 -centrimo-score $options_type_cond.centrimo_score
68 #end if
69 #if str($options_type_cond.centrimo_maxreg) != "0":
70 -centrimo-maxreg $options_type_cond.centrimo_maxreg
71 #end if
72 #if str($options_type_cond.centrimo_ethresh) != "0":
73 -centrimo-ethresh $options_type_cond.centrimo_ethresh
74 #end if
75 #if str($options_type_cond.centrimo_noseq) == "true":
76 -centrimo-noseq
77 #end if
78 #if str($options_type_cond.centrimo_flip) == "true":
79 -centrimo-flip
80 #end if
81 -spamo-skip
82 -fimo-skip
83 #end if
84 &>meme_chip_log.txt;
85 if [[ $? -ne 0 ]]; then
86 cp meme_chip_log.txt '$output';
87 exit 1;
88 fi]]></command>
89 <inputs>
90 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
91 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
92 <option value="dna" selected="true">DNA</option>
93 <option value="rna">RNA</option>
94 </param>
95 <param name="meme_motif_databases" type="select" label="MEME motif database">
96 <options from_data_table="meme_motif_databases">
97 <filter type="sort_by" column="1"/>
98 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
99 </options>
100 </param>
101 <conditional name="options_type_cond">
102 <param name="options_type" type="select" label="Options Configuration">
103 <option value="basic" selected="true">Basic</option>
104 <option value="advanced">Advanced</option>
105 </param>
106 <when value="basic"/>
107 <when value="advanced">
108 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
109 <option value="0">0-order model of sequences</option>
110 <option value="1" selected="True">1st order model of sequences</option>
111 <option value="2">2nd order model of sequences</option>
112 <option value="3">3rd order model of sequences</option>
113 <option value="4">4th order model of sequences</option>
114 </param>
115 <conditional name="subsampling_cond">
116 <param name="subsampling" type="select" label="Should subsampling be random?" help="Select 'No' if your input sequences are sorted in order of confidence (best to worst)">
117 <option value="yes" selected="true">Yes</option>
118 <option value="no">No</option>
119 </param>
120 <when value="yes">
121 <param name="seed" type="integer" value="0" min="0" label="Seed for the randomized selection of sequences" help="Zero value indicates random seeding"/>
122 </when>
123 <when value="no"/>
124 </conditional>
125 <param name="nmeme" type="integer" value="0" min="0" label="Limit of sequences to pass to MEME" help="Zero value has no effect"/>
126 <param name="ccut" type="integer" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/>
127 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
128 <param name="group_weak" type="float" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
129 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
130 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
131 <option value="oops" selected="True">One occurance per sequence</option>
132 <option value="zoops">Zero or one occurances per sequence</option>
133 <option value="anr">Any number of repititions</option>
134 </param>
135 <param name="meme_minw" type="integer" value="0" min="0" label="Minimum motif width"/>
136 <param name="meme_maxw" type="integer" value="0" min="0" label="Maximum motif width"/>
137 <param name="meme_nmotifs" type="integer" value="0" min="0" label="Maximum number of motifs to find"/>
138 <param name="meme_minsites" type="integer" value="0" min="0" label="Minimum number of sites per motif"/>
139 <param name="meme_maxsites" type="integer" value="0" label="Maximum number of sites per motif"/>
140 <param name="meme_pal" type="boolean" truevalue="true" falsevalue="" checked="False" label="Look for palindromes only"/>
141 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
142 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
143 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/>
144 <param name="centrimo_score" type="integer" value="0" min="0" label="Minimum allowed CentriMo match score"/>
145 <param name="centrimo_maxreg" type="integer" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
146 <param name="centrimo_ethresh" type="integer" value="0" min="0" label="CentriMo E-value threshold for reporting" />
147 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
148 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
149 </when>
150 </conditional>
151 <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">
152 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
153 </param>
154 </inputs>
155 <outputs>
156 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/>
157 </outputs>
158 <tests>
159 <test>
160 <param name="input" value="extract_genomic_dna.fa" ftype="fasta"/>
161 <output name="output" file="sample_output.html" ftype="html"/>
162 </test>
163 </tests>
164 <help>
165 .. class:: warningmark
166
167 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
168 Before using, be sure to review, agree, and comply with the license.**
169
170 MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.
171
172 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
173
174 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
175 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
176 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
177 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
178 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
179 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
180 of occurrences, and description for each motif.
181
182 .. class:: infomark
183
184 For detailed information on MEME, click here_, or view the license_.
185
186 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
187 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
188
189 </help>
190 <citations>
191 <citation type="bibtex">
192 @article{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
193 author = {Bailey,Timothy L. and Elkan, Charles},
194 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
195 year = {1994},
196 eprint = {None},
197 url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
198 }</citation>
199 </citations>
200 </tool>