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comparison meme_chip.xml @ 3:8d3877046d78 draft

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author iuc
date Thu, 15 Mar 2018 13:15:53 -0400
parents fd58302909b8
children ff7dc6057652
comparison
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2:34a8d71a6ee2 3:8d3877046d78
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 #import os
9 #set primary_output = $os.path.join($output.files_path, "index.html")
8 #set options_type = $options_type_cond.options_type 10 #set options_type = $options_type_cond.options_type
9 meme-chip $input 11 meme-chip $input
10 -noecho 12 -noecho
11 -db $meme_motif_databases.fields.path 13 #if str($control) not in ['', 'None']:
14 -neg '$control'
15 #end if
12 #if $sequence_alphabet == 'dna': 16 #if $sequence_alphabet == 'dna':
13 -dna 17 -dna
14 #else: 18 #else:
15 -rna 19 -rna
16 -norc
17 #end if 20 #end if
18 -o '$output.files_path' 21 -o '$output.files_path'
19
20 #if str($options_type)=='advanced': 22 #if str($options_type)=='advanced':
23 #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
24 ## FIXME: CentriMo cannot be run, See the comments in the input tag section.
25 ## #if str($run_centrimo) == "yes":
26 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
27 ## #if str($options_type_cond.run_centrimo_cond.centrimo_local) == "true":
28 ## -centrimo-local
29 ## #end if
30 ## #if str($options_type_cond.run_centrimo_cond.centrimo_score) != "0":
31 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
32 ## #end if
33 ## #if str($options_type_cond.run_centrimo_cond.centrimo_maxreg) != "0":
34 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
35 ## #end if
36 ## #if str($options_type_cond.run_centrimo_cond.centrimo_ethresh) != "0":
37 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
38 ## #end if
39 ## #if str($options_type_cond.run_centrimo_cond.centrimo_noseq) == "true":
40 ## -centrimo-noseq
41 ## #end if
42 ## #if str($options_type_cond.run_centrimo_cond.centrimo_flip) == "true":
43 ## -centrimo-flip
44 ## #end if
45 ## #end if
46 #if str($options_type_cond.search_given_strand) == "true":
47 -norc
48 #end if
21 -order $options_type_cond.background_model_order 49 -order $options_type_cond.background_model_order
22 #if str($options_type_cond.subsampling) == "no": 50 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
23 -norand 51 -norand
24 #end if
25 #if str($options_type_cond.subsampling_cond.subsampling) != "yes":
26 #set seed = $options_type_cond.subsampling_cond.subsampling.seed 52 #set seed = $options_type_cond.subsampling_cond.subsampling.seed
27 #if str($seed) != "0": 53 #if str($seed) != "0":
28 -seed $options_type_cond.subsampling_cond.subsampling.seed 54 -seed $options_type_cond.subsampling_cond.subsampling.seed
29 #end if 55 #end if
30 #end if 56 #end if
37 -group-thresh $options_type_cond.group_threash 63 -group-thresh $options_type_cond.group_threash
38 #if str($options_type_cond.group_weak) != "0": 64 #if str($options_type_cond.group_weak) != "0":
39 -group-weak $options_type_cond.group_weak 65 -group-weak $options_type_cond.group_weak
40 #end if 66 #end if
41 -filter-thresh $options_type_cond.filter_threash 67 -filter-thresh $options_type_cond.filter_threash
68 #if str($options_type_cond.old_clustering) == "true":
69 -old-clustering
70 #end if
42 -meme-mod $options_type_cond.meme_mod 71 -meme-mod $options_type_cond.meme_mod
43 #if str($options_type_cond.meme_minw) != "0": 72 #if str($options_type_cond.meme_minw) != "0":
44 -meme-minw $options_type_cond.meme_minw 73 -meme-minw $options_type_cond.meme_minw
45 #end if 74 #end if
46 #if str($options_type_cond.meme_maxw) != "0": 75 #if str($options_type_cond.meme_maxw) != "0":
58 #if str($options_type_cond.meme_pal) == "true": 87 #if str($options_type_cond.meme_pal) == "true":
59 -meme-pal 88 -meme-pal
60 #end if 89 #end if
61 -dreme-e $options_type_cond.dreme_e 90 -dreme-e $options_type_cond.dreme_e
62 -dreme-m $options_type_cond.dreme_m 91 -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 92 -spamo-skip
82 -fimo-skip 93 -fimo-skip
83 #end if 94 #end if
84 &>meme_chip_log.txt; 95 &>meme_chip_log.txt;
85 if [[ $? -ne 0 ]]; then 96 if [[ $? -ne 0 ]]; then
86 cp meme_chip_log.txt '$output'; 97 cp meme_chip_log.txt '$output';
87 exit 1; 98 exit 1;
88 fi]]></command> 99 fi
100 && rm '$output'
101 && ln -s $primary_output '$output'
102 ]]></command>
89 <inputs> 103 <inputs>
90 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/> 104 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
105 <param name="control" type="data" format="fasta" optional="true" label="Control sequences" help="If no selection, positive sequences in the input are shuffled to create the negative set"/>
91 <param name="sequence_alphabet" type="select" label="Sequence alphabet"> 106 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
92 <option value="dna" selected="true">DNA</option> 107 <option value="dna" selected="true">DNA</option>
93 <option value="rna">RNA</option> 108 <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> 109 </param>
101 <conditional name="options_type_cond"> 110 <conditional name="options_type_cond">
102 <param name="options_type" type="select" label="Options Configuration"> 111 <param name="options_type" type="select" label="Options Configuration">
103 <option value="basic" selected="true">Basic</option> 112 <option value="basic" selected="true">Basic</option>
104 <option value="advanced">Advanced</option> 113 <option value="advanced">Advanced</option>
105 </param> 114 </param>
106 <when value="basic"/> 115 <when value="basic"/>
107 <when value="advanced"> 116 <when value="advanced">
117 <!--
118 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
119 <conditional name="run_centrimo_cond">
120 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
121 <option value="yes" selected="true">Yes</option>
122 <option value="no">No</option>
123 </param>
124 <when value="yes">
125
126 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
127 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
128 select list is changed. This composition used to work (see Examples->Dynamic Options section of
129 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in
130 the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
131
132 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
133 <options from_data_table="meme_motif_databases">
134 <filter type="sort_by" column="1"/>
135 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
136 </options>
137 </param>
138 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/>
139 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/>
140 <param name="centrimo_score" type="integer" value="0" min="0" label="Minimum allowed CentriMo match score"/>
141 <param name="centrimo_maxreg" type="integer" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
142 <param name="centrimo_ethresh" type="integer" value="0" min="0" label="CentriMo E-value threshold for reporting" />
143 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
144 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
145 </when>
146 <when value="no"/>
147 </conditional>
148 -->
108 <param name="background_model_order" type="select" label="Select the order of the Markov background model"> 149 <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> 150 <option value="0">0-order model of sequences</option>
110 <option value="1" selected="True">1st order model of sequences</option> 151 <option value="1" selected="True">1st order model of sequences</option>
111 <option value="2">2nd order model of sequences</option> 152 <option value="2">2nd order model of sequences</option>
112 <option value="3">3rd order model of sequences</option> 153 <option value="3">3rd order model of sequences</option>
113 <option value="4">4th order model of sequences</option> 154 <option value="4">4th order model of sequences</option>
114 </param> 155 </param>
156 <param name="nmeme" type="integer" value="0" min="0" label="Limit of sequences to pass to MEME" help="Zero value has no effect"/>
115 <conditional name="subsampling_cond"> 157 <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)"> 158 <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> 159 <option value="yes" selected="true">Yes</option>
118 <option value="no">No</option> 160 <option value="no">No</option>
119 </param> 161 </param>
120 <when value="yes"> 162 <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"/> 163 <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> 164 </when>
123 <when value="no"/> 165 <when value="no"/>
124 </conditional> 166 </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"/> 167 <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" /> 168 <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"/> 169 <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"/> 170 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
171 <param name="search_given_strand" type="boolean" truevalue="true" falsevalue="" checked="False" label="Search given strand only"/>
172 <param name="old_clustering" type="boolean" truevalue="true" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
130 <param name="meme_mod" type="select" label="What is the expected motif site distribution?"> 173 <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> 174 <option value="oops" selected="True">One occurance per sequence</option>
132 <option value="zoops">Zero or one occurances per sequence</option> 175 <option value="zoops">Zero or one occurances per sequence</option>
133 <option value="anr">Any number of repititions</option> 176 <option value="anr">Any number of repititions</option>
134 </param> 177 </param>
138 <param name="meme_minsites" type="integer" value="0" min="0" label="Minimum number of sites per motif"/> 181 <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"/> 182 <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"/> 183 <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"/> 184 <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" /> 185 <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> 186 </when>
150 </conditional> 187 </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"> 188 <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> 189 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
153 </param> 190 </param>
186 .. _here: http://meme-suite.org/doc/meme.html?man_type=web 223 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
187 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web 224 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
188 225
189 </help> 226 </help>
190 <citations> 227 <citations>
191 <citation type="bibtex"> 228 <citation type="doi">10.1093/bioinformatics/btr189</citation>
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> 229 </citations>
200 </tool> 230 </tool>
231