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comparison meme_chip.xml @ 5:ff7dc6057652 draft

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author iuc
date Mon, 16 Apr 2018 11:27:00 -0400
parents 8d3877046d78
children 444093446b0b
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4:3eee5fd08dac 5:ff7dc6057652
1 <tool id="meme_chip" name="MEME-ChIP" version="4.12.0"> 1 <tool id="meme_chip" name="MEME-ChIP" version="4.11.2">
2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description> 2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</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 <code file="get_meme_motif_databases.py" />
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #import os 9 #import os
9 #set primary_output = $os.path.join($output.files_path, "index.html") 10 #set primary_output = $os.path.join($output.files_path, "index.html")
10 #set options_type = $options_type_cond.options_type 11 #set options_type = $options_type_cond.options_type
11 meme-chip $input 12 meme-chip '$input'
12 -noecho 13 -noecho
13 #if str($control) not in ['', 'None']: 14 #if str($control):
14 -neg '$control' 15 -neg '$control'
15 #end if
16 #if $sequence_alphabet == 'dna':
17 -dna
18 #else:
19 -rna
20 #end if 16 #end if
21 -o '$output.files_path' 17 -o '$output.files_path'
22 #if str($options_type)=='advanced': 18 #if str($options_type)=='advanced':
23 #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo 19 ## FIXME: CentriMo cannot be run, See the comments in the input section.
24 ## FIXME: CentriMo cannot be run, See the comments in the input tag section. 20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
25 ## #if str($run_centrimo) == "yes": 21 ## #if str($run_centrimo) == "yes":
26 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path 22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
27 ## #if str($options_type_cond.run_centrimo_cond.centrimo_local) == "true": 23 ## #if str($options_type_cond.run_centrimo_cond.centrimo_local):
28 ## -centrimo-local 24 ## -centrimo-local
29 ## #end if 25 ## #end if
30 ## #if str($options_type_cond.run_centrimo_cond.centrimo_score) != "0": 26 ## #if str($options_type_cond.run_centrimo_cond.centrimo_score):
31 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score 27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
32 ## #end if 28 ## #end if
33 ## #if str($options_type_cond.run_centrimo_cond.centrimo_maxreg) != "0": 29 ## #if str($options_type_cond.run_centrimo_cond.centrimo_maxreg):
34 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg 30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
35 ## #end if 31 ## #end if
36 ## #if str($options_type_cond.run_centrimo_cond.centrimo_ethresh) != "0": 32 ## #if str($options_type_cond.run_centrimo_cond.centrimo_ethresh):
37 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh 33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
38 ## #end if 34 ## #end if
39 ## #if str($options_type_cond.run_centrimo_cond.centrimo_noseq) == "true": 35 ## #if str($options_type_cond.run_centrimo_cond.centrimo_noseq):
40 ## -centrimo-noseq 36 ## -centrimo-noseq
41 ## #end if 37 ## #end if
42 ## #if str($options_type_cond.run_centrimo_cond.centrimo_flip) == "true": 38 ## #if str($options_type_cond.run_centrimo_cond.centrimo_flip):
43 ## -centrimo-flip 39 ## -centrimo-flip
44 ## #end if 40 ## #end if
45 ## #end if 41 ## #end if
46 #if str($options_type_cond.search_given_strand) == "true": 42 #if str($options_type_cond.search_given_strand):
47 -norc 43 -norc
48 #end if 44 #end if
49 -order $options_type_cond.background_model_order 45 -order $options_type_cond.background_model_order
50 #if str($options_type_cond.subsampling_cond.subsampling) == "no": 46 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
51 -norand 47 -norand
52 #set seed = $options_type_cond.subsampling_cond.subsampling.seed 48 #set seed = $options_type_cond.subsampling_cond.subsampling.seed
53 #if str($seed) != "0": 49 #if str($seed):
54 -seed $options_type_cond.subsampling_cond.subsampling.seed 50 -seed $options_type_cond.subsampling_cond.subsampling.seed
55 #end if 51 #end if
56 #end if 52 #end if
57 #if str($options_type_cond.nmeme) != "0": 53 #if str($options_type_cond.nmeme):
58 -nmeme $options_type_cond.nmeme 54 -nmeme $options_type_cond.nmeme
59 #end if 55 #end if
60 #if str($options_type_cond.ccut) != "0": 56 #if str($options_type_cond.ccut):
61 -ccut $options_type_cond.ccut 57 -ccut $options_type_cond.ccut
62 #end if 58 #end if
63 -group-thresh $options_type_cond.group_threash 59 -group-thresh $options_type_cond.group_threash
64 #if str($options_type_cond.group_weak) != "0": 60 #if str($options_type_cond.group_weak):
65 -group-weak $options_type_cond.group_weak 61 -group-weak $options_type_cond.group_weak
66 #end if 62 #end if
67 -filter-thresh $options_type_cond.filter_threash 63 -filter-thresh $options_type_cond.filter_thresh
68 #if str($options_type_cond.old_clustering) == "true": 64 #if str($options_type_cond.old_clustering):
69 -old-clustering 65 -old-clustering
70 #end if 66 #end if
71 -meme-mod $options_type_cond.meme_mod 67 -meme-mod $options_type_cond.meme_mod
72 #if str($options_type_cond.meme_minw) != "0": 68 #if str($options_type_cond.meme_minw):
73 -meme-minw $options_type_cond.meme_minw 69 -meme-minw $options_type_cond.meme_minw
74 #end if 70 #end if
75 #if str($options_type_cond.meme_maxw) != "0": 71 #if str($options_type_cond.meme_maxw):
76 -meme-maxw $options_type_cond.meme_maxw 72 -meme-maxw $options_type_cond.meme_maxw
77 #end if 73 #end if
78 #if str($options_type_cond.meme_nmotifs) != '0': 74 #if str($options_type_cond.meme_nmotifs):
79 -meme-nmotifs $options_type_cond.meme_nmotifs 75 -meme-nmotifs $options_type_cond.meme_nmotifs
80 #end if 76 #end if
81 #if str($options_type_cond.meme_minsites) != "0": 77 #if str($options_type_cond.meme_minsites):
82 -meme-minsites $options_type_cond.meme_minsites 78 -meme-minsites $options_type_cond.meme_minsites
83 #end if 79 #end if
84 #if str($options_type_cond.meme_maxsites) != "0": 80 #if str($options_type_cond.meme_maxsites):
85 -meme-maxsites $options_type_cond.meme_maxsites 81 -meme-maxsites $options_type_cond.meme_maxsites
86 #end if 82 #end if
87 #if str($options_type_cond.meme_pal) == "true": 83 #if str($options_type_cond.meme_pal):
88 -meme-pal 84 -meme-pal
89 #end if 85 #end if
90 -dreme-e $options_type_cond.dreme_e 86 -dreme-e $options_type_cond.dreme_e
91 -dreme-m $options_type_cond.dreme_m 87 -dreme-m $options_type_cond.dreme_m
92 -spamo-skip 88 -spamo-skip
93 -fimo-skip 89 -fimo-skip
94 #end if 90 #end if
95 &>meme_chip_log.txt;
96 if [[ $? -ne 0 ]]; then
97 cp meme_chip_log.txt '$output';
98 exit 1;
99 fi
100 && rm '$output' 91 && rm '$output'
101 && ln -s $primary_output '$output' 92 && ln -s $primary_output '$output'
102 ]]></command> 93 ]]></command>
103 <inputs> 94 <inputs>
104 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/> 95 <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"/> 96 <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"/>
106 <param name="sequence_alphabet" type="select" label="Sequence alphabet"> 97 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
107 <option value="dna" selected="true">DNA</option> 98 <option value="-dna" selected="true">DNA</option>
108 <option value="rna">RNA</option> 99 <option value="-rna">RNA</option>
109 </param> 100 </param>
110 <conditional name="options_type_cond"> 101 <conditional name="options_type_cond">
111 <param name="options_type" type="select" label="Options Configuration"> 102 <param name="options_type" type="select" label="Options Configuration">
112 <option value="basic" selected="true">Basic</option> 103 <option value="basic" selected="true">Basic</option>
113 <option value="advanced">Advanced</option> 104 <option value="advanced">Advanced</option>
135 <validator type="no_options" message="No MEME motif databases are available for the selected input"/> 126 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
136 </options> 127 </options>
137 </param> 128 </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)"/> 129 <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"/> 130 <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"/> 131 <param name="centrimo_score" type="integer" optional="true" 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"/> 132 <param name="centrimo_maxreg" type="integer" optional="true" 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" /> 133 <param name="centrimo_ethresh" type="integer" optional="true" 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"/> 134 <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"/> 135 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
145 </when> 136 </when>
146 <when value="no"/> 137 <when value="no"/>
147 </conditional> 138 </conditional>
151 <option value="1" selected="True">1st order model of sequences</option> 142 <option value="1" selected="True">1st order model of sequences</option>
152 <option value="2">2nd order model of sequences</option> 143 <option value="2">2nd order model of sequences</option>
153 <option value="3">3rd order model of sequences</option> 144 <option value="3">3rd order model of sequences</option>
154 <option value="4">4th order model of sequences</option> 145 <option value="4">4th order model of sequences</option>
155 </param> 146 </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"/> 147 <param name="nmeme" type="integer" optional="true" value="0" min="0" label="Limit of sequences to pass to MEME" help="Zero value has no effect"/>
157 <conditional name="subsampling_cond"> 148 <conditional name="subsampling_cond">
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)"> 149 <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)">
159 <option value="yes" selected="true">Yes</option> 150 <option value="yes" selected="true">Yes</option>
160 <option value="no">No</option> 151 <option value="no">No</option>
161 </param> 152 </param>
162 <when value="yes"> 153 <when value="yes">
163 <param name="seed" type="integer" value="0" min="0" label="Seed for the randomized selection of sequences" help="Zero value indicates random seeding"/> 154 <param name="seed" type="integer" optional="true" value="0" min="0" label="Seed for the randomized selection of sequences" help="Zero value indicates random seeding"/>
164 </when> 155 </when>
165 <when value="no"/> 156 <when value="no"/>
166 </conditional> 157 </conditional>
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"/> 158 <param name="ccut" type="integer" optional="true" 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"/>
168 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" /> 159 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
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"/> 160 <param name="group_weak" type="float" optional="true" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
170 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/> 161 <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"/> 162 <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"/> 163 <param name="old_clustering" type="boolean" truevalue="true" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
173 <param name="meme_mod" type="select" label="What is the expected motif site distribution?"> 164 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
174 <option value="oops" selected="True">One occurance per sequence</option> 165 <option value="oops" selected="True">One occurance per sequence</option>
175 <option value="zoops">Zero or one occurances per sequence</option> 166 <option value="zoops">Zero or one occurances per sequence</option>
176 <option value="anr">Any number of repititions</option> 167 <option value="anr">Any number of repititions</option>
177 </param> 168 </param>
178 <param name="meme_minw" type="integer" value="0" min="0" label="Minimum motif width"/> 169 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/>
179 <param name="meme_maxw" type="integer" value="0" min="0" label="Maximum motif width"/> 170 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/>
180 <param name="meme_nmotifs" type="integer" value="0" min="0" label="Maximum number of motifs to find"/> 171 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/>
181 <param name="meme_minsites" type="integer" value="0" min="0" label="Minimum number of sites per motif"/> 172 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/>
182 <param name="meme_maxsites" type="integer" value="0" label="Maximum number of sites per motif"/> 173 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/>
183 <param name="meme_pal" type="boolean" truevalue="true" falsevalue="" checked="False" label="Look for palindromes only"/> 174 <param name="meme_pal" type="boolean" truevalue="true" falsevalue="" checked="False" label="Look for palindromes only"/>
184 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/> 175 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
185 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" /> 176 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
186 </when> 177 </when>
187 </conditional> 178 </conditional>
192 <outputs> 183 <outputs>
193 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/> 184 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/>
194 </outputs> 185 </outputs>
195 <tests> 186 <tests>
196 <test> 187 <test>
197 <param name="input" value="extract_genomic_dna.fa" ftype="fasta"/> 188 <param name="input" value="input1.fasta" ftype="fasta"/>
198 <output name="output" file="sample_output.html" ftype="html"/> 189 <param name="non_commercial_use" value="True"/>
190 <output name="output" file="output1.html" ftype="html" compare="contains"/>
191 </test>
192 <test>
193 <param name="input" value="input1.fasta" ftype="fasta"/>
194 <param name="sequence_alphabet" value="rna"/>
195 <param name="options_type" value="advanced"/>
196 <param name="background_model_order" value="0"/>
197 <param name="non_commercial_use" value="True"/>
198 <output name="output" file="output1.html" ftype="html" compare="contains"/>
199 </test> 199 </test>
200 </tests> 200 </tests>
201 <help> 201 <help>
202 .. class:: warningmark 202 .. class:: warningmark
203 203