|
16
|
1 <tool id="meme_chip_wrapper" name="meme-chip" version="1.2.3">
|
|
11
|
2 <requirements>
|
|
|
3 <requirement type="package" version="4.9.0">meme</requirement>
|
|
|
4 </requirements>
|
|
|
5 <description></description>
|
|
|
6 <version_command>echo "MEME version r4.9.0"</version_command>
|
|
|
7 <command> meme-chip $input_file -o ${memechip_out.files_path}
|
|
|
8 #for p in str.split($motif_dbs.fields.path,","):
|
|
|
9 -db $p
|
|
|
10 #end for
|
|
|
11
|
|
|
12 #if str( $options_type.options_type_selector ) == 'advanced':
|
|
|
13 #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
|
|
|
14 -bfile "${ str( $options_type.bg_type.bfile ) }"
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if str( $options_type.ccut ) != '-1':
|
|
|
18 -ccut "${ str( $options_type.ccut ) }"
|
|
|
19 #end if
|
|
|
20
|
|
|
21 #if str( $options_type.time ) != '-1':
|
|
|
22 -time "${ str( $options_type.time ) }"
|
|
|
23 #end if
|
|
|
24
|
|
|
25 -desc "${ str( $options_type.desc ) }"
|
|
|
26
|
|
|
27 #if str( $options_type.meme_mod ) != '':
|
|
|
28 -meme-mod "${ str($options_type.meme_mod) }"
|
|
|
29 #end if
|
|
|
30
|
|
|
31 #if str( $options_type.meme_minw ) != '-1':
|
|
|
32 -meme-minw "${ str($options_type.meme_minw) }"
|
|
|
33 #end if
|
|
|
34
|
|
|
35 #if str( $options_type.meme_maxw ) != '-1':
|
|
|
36 -meme-maxw "${ str($options_type.meme_maxw) }"
|
|
|
37 #end if
|
|
|
38
|
|
|
39 #if str( $options_type.meme_nmotifs ) != '-1':
|
|
|
40 -meme-nmotifs "${ str($options_type.meme_nmotifs) }"
|
|
|
41 #end if
|
|
|
42
|
|
|
43 #if str( $options_type.meme_minsites ) != '-1':
|
|
|
44 -meme-minsites "${ str($options_type.meme_minsites) }"
|
|
|
45 #end if
|
|
|
46
|
|
|
47 #if str( $options_type.meme_maxsites ) != '-1':
|
|
|
48 -meme-maxsites "${ str($options_type.meme_maxsites) }"
|
|
|
49 #end if
|
|
|
50
|
|
|
51 #if $options_type.meme_pal:
|
|
|
52 -meme-pal "${ str($options_type.meme_pal) }"
|
|
|
53 #end if
|
|
|
54
|
|
|
55 #if str( $options_type.dreme_e ) != '-1.0':
|
|
|
56 -dreme-e "${ str($options_type.dreme_e) }"
|
|
|
57 #end if
|
|
|
58
|
|
|
59 #if str( $options_type.dreme_m ) != '-1':
|
|
|
60 -dreme-m "${ str($options_type.dreme_m) }"
|
|
|
61 #end if
|
|
|
62
|
|
|
63 #if str($options_type.centrimo_score) != '-1.0':
|
|
|
64 -centrimo-score "${ str($options_type.centrimo_score) }"
|
|
|
65 #end if
|
|
|
66
|
|
|
67 #if str( $options_type.centrimo_maxreg ) != '-1':
|
|
|
68 -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }"
|
|
|
69 #end if
|
|
|
70
|
|
|
71 #if str( $options_type.centrimo_ethresh ) != '-1.0':
|
|
|
72 -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }"
|
|
|
73 #end if
|
|
|
74
|
|
|
75 #if $options_type.centrimo_noseq:
|
|
|
76 -centrimo-noseq
|
|
|
77 #end if
|
|
|
78
|
|
|
79 #end if
|
|
|
80 <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
|
|
|
81 2>&1 || echo "Error running MEME."
|
|
|
82 <!--&& mv ${html_outfile.files_path}/index.html ${html_outfile}-->
|
|
|
83 <!--&& zip -r result $html_outfile.files_path-->
|
|
|
84 && cd ${memechip_out.files_path}
|
|
|
85 && zip -rp memechip_out ./
|
|
|
86 && mv memechip_out.zip ${memechip_out}
|
|
|
87 </command>
|
|
|
88 <inputs>
|
|
|
89 <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
|
|
|
90 <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases">
|
|
|
91 <options from_data_table="meme_chip_motifs">
|
|
|
92 <filter type="sort_by" column="1"/>
|
|
|
93 <validator type="no_options" message="No indexes are available for the selected dataset"/>
|
|
|
94 </options>
|
|
|
95
|
|
|
96 </param>
|
|
|
97 <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="True">
|
|
|
98 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
|
|
|
99 </param>
|
|
|
100 <conditional name="options_type">
|
|
|
101 <param name="options_type_selector" type="select" label="Options Configuration">
|
|
|
102 <option value="basic" selected="true">Basic</option>
|
|
|
103 <option value="advanced">Advanced</option>
|
|
|
104 </param>
|
|
|
105 <when value="basic">
|
|
|
106 <!-- do nothing here -->
|
|
|
107 </when>
|
|
|
108 <when value="advanced">
|
|
|
109 <!--bfile-->
|
|
|
110 <conditional name="bg_type">
|
|
|
111 <param name="bg_type_selector" type="select" label="Custom background">
|
|
|
112 <option value="bg_default" selected="True">Default Background</option>
|
|
|
113 <option value="bg_user">Background in your History</option>
|
|
|
114 </param>
|
|
|
115 <when value="bg_default">
|
|
|
116 <!--do nothing here-->
|
|
|
117 </when>
|
|
|
118 <when value="bg_user">
|
|
|
119 <param name="bfile" type="data" label="-bfile: Background File" />
|
|
|
120 </when>
|
|
|
121 </conditional>
|
|
|
122 <!--ccut-->
|
|
|
123 <param name="ccut" type="integer" value="-1" label="-ccut: Max size of a seq before it is cut down; 0: do not cut; -1: Default behaviour" />
|
|
|
124 <!--tine-->
|
|
|
125 <param name="time" type="integer" value="-1" label="-time: Maximum time (minutes) that this program has to run and create output in; -1: no limit" />
|
|
|
126 <!--desc-->
|
|
|
127 <param name="desc" type="text" value="Galaxy MEME-Chip" label="-desc: Description of the analysis" >
|
|
|
128 <sanitizer>
|
|
|
129 <valid initial="string.printable">
|
|
|
130 <remove value="'"/>
|
|
|
131 </valid>
|
|
|
132 <mapping initial="none">
|
|
|
133 <add source="'" target=""/>
|
|
|
134 </mapping>
|
|
|
135 </sanitizer>
|
|
|
136 </param>
|
|
|
137 <!--MEME options-->
|
|
|
138 <param name="meme_mod" type="select" label="-meme-mod: Sites used in a single sequence" >
|
|
|
139 <option value="" selected="True"/>
|
|
|
140 <option value="oops" />
|
|
|
141 <option value="zoops" />
|
|
|
142 <option value="anr" />
|
|
|
143 </param>
|
|
|
144 <param name="meme_minw" type="integer" value="-1" label="-meme-minw: minimum motif width; -1: Default behaviour" />
|
|
|
145 <param name="meme_maxw" type="integer" value="-1" label="-meme-maxw: maximum motif width; -1: Default behaviour" />
|
|
|
146 <param name="meme_nmotifs" type="integer" value="-1" label="-meme-nmotifs: maximum number of motifs to find; -1: Default behaviour" />
|
|
|
147 <param name="meme_minsites" type="integer" value="-1" label="-meme-minsites: minimum number of sites per motif; -1: Default behaviour" />
|
|
|
148 <param name="meme_maxsites" type="integer" value="-1" label="-meme-maxsites: maximum number of sites per motif; -1: Default behaviour" />
|
|
|
149 <param name="meme_pal" type="boolean" label="-meme-pal: look for palindromes only" />
|
|
|
150 <!--DREME options-->
|
|
|
151 <param name="dreme_e" type="float" value="-1" label="-dreme-e: stop searching after reaching this E-value threshold; -1: Default behaviour" />
|
|
|
152 <param name="dreme_m" type="integer" value="-1" label="-dreme-e: stop searching after finding this many motifs; -1: Default behaviour" />
|
|
|
153 <!--CentriMo options-->
|
|
|
154 <param name="centrimo_score" type="float" value="-1" label="-centrimo-score: set the minimum allowed match score; -1: Default behaviour" />
|
|
|
155 <param name="centrimo_maxreg" type="integer" value="-1" label="-centrimo-maxreg: set the maximum region size to be considered; -1: Default behaviour" />
|
|
|
156 <param name="centrimo_ethresh" type="float" value="-1" label="-centrimo-ethresh: set the E-value threshold for reporting; -1: Default behaviour" />
|
|
|
157 <param name="centrimo_noseq" type="boolean" label="-centrimo-noseq: don't store sequence IDs in the output" />
|
|
|
158
|
|
|
159 </when>
|
|
|
160 </conditional>
|
|
|
161 </inputs>
|
|
|
162 <outputs>
|
|
|
163 <!--<data format="html" name="html_outfile" label="index" />-->
|
|
|
164 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
|
|
|
165 <data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />
|
|
|
166 </outputs>
|
|
|
167
|
|
|
168
|
|
|
169 <tests>
|
|
|
170 <test>
|
|
|
171 <param name="input_file" value="extract_genomic_dna.fa" />
|
|
|
172 <output name="html_file" file="sample_output.html" ftype="html" />
|
|
|
173 </test>
|
|
|
174 </tests>
|
|
|
175
|
|
|
176 <help>
|
|
|
177
|
|
|
178 .. class:: infomark
|
|
|
179
|
|
|
180 After the job finishes, save the zip file, unzip and open "index.html"
|
|
|
181
|
|
|
182 The actual meme-chip command is displayed under "Command line summary"
|
|
|
183
|
|
|
184 Defaults:
|
|
|
185 http://meme.nbcr.net/meme/doc/meme-chip.html
|
|
|
186
|
|
|
187 </help>
|
|
|
188 </tool>
|
