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comparison meme_chip_wrapper.xml @ 18:2948554ae3d7 draft default tip

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added nmeme option
author kevyin
date Thu, 22 Nov 2012 20:27:29 -0500
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17:5bb9eb050e57 18:2948554ae3d7
1 <tool id="meme_chip_wrapper" name="meme-chip" version="1.2.4">
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( $options_type.nmeme) != '-1':
18 -nmeme "${ str( $options_type.nmeme ) }"
19 #end if
20
21 #if str( $options_type.ccut ) != '-1':
22 -ccut "${ str( $options_type.ccut ) }"
23 #end if
24
25 #if str( $options_type.time ) != '-1':
26 -time "${ str( $options_type.time ) }"
27 #end if
28
29 -desc "${ str( $options_type.desc ) }"
30
31 #if str( $options_type.meme_mod ) != '':
32 -meme-mod "${ str($options_type.meme_mod) }"
33 #end if
34
35 #if str( $options_type.meme_minw ) != '-1':
36 -meme-minw "${ str($options_type.meme_minw) }"
37 #end if
38
39 #if str( $options_type.meme_maxw ) != '-1':
40 -meme-maxw "${ str($options_type.meme_maxw) }"
41 #end if
42
43 #if str( $options_type.meme_nmotifs ) != '-1':
44 -meme-nmotifs "${ str($options_type.meme_nmotifs) }"
45 #end if
46
47 #if str( $options_type.meme_minsites ) != '-1':
48 -meme-minsites "${ str($options_type.meme_minsites) }"
49 #end if
50
51 #if str( $options_type.meme_maxsites ) != '-1':
52 -meme-maxsites "${ str($options_type.meme_maxsites) }"
53 #end if
54
55 #if $options_type.meme_pal:
56 -meme-pal "${ str($options_type.meme_pal) }"
57 #end if
58
59 #if str( $options_type.dreme_e ) != '-1.0':
60 -dreme-e "${ str($options_type.dreme_e) }"
61 #end if
62
63 #if str( $options_type.dreme_m ) != '-1':
64 -dreme-m "${ str($options_type.dreme_m) }"
65 #end if
66
67 #if str($options_type.centrimo_score) != '-1.0':
68 -centrimo-score "${ str($options_type.centrimo_score) }"
69 #end if
70
71 #if str( $options_type.centrimo_maxreg ) != '-1':
72 -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }"
73 #end if
74
75 #if str( $options_type.centrimo_ethresh ) != '-1.0':
76 -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }"
77 #end if
78
79 #if $options_type.centrimo_noseq:
80 -centrimo-noseq
81 #end if
82
83 #end if
84 <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
85 2&gt;&amp;1 || echo "Error running MEME."
86 <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}-->
87 <!--&amp;&amp; zip -r result $html_outfile.files_path-->
88 &amp;&amp; cd ${memechip_out.files_path}
89 &amp;&amp; zip -rp memechip_out ./
90 &amp;&amp; mv memechip_out.zip ${memechip_out}
91 </command>
92 <inputs>
93 <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
94 <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases">
95 <options from_data_table="meme_chip_motifs">
96 <filter type="sort_by" column="1"/>
97 <validator type="no_options" message="No indexes are available for the selected dataset"/>
98 </options>
99
100 </param>
101 <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">
102 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
103 </param>
104 <conditional name="options_type">
105 <param name="options_type_selector" type="select" label="Options Configuration">
106 <option value="basic" selected="true">Basic</option>
107 <option value="advanced">Advanced</option>
108 </param>
109 <when value="basic">
110 <!-- do nothing here -->
111 </when>
112 <when value="advanced">
113 <!--bfile-->
114 <conditional name="bg_type">
115 <param name="bg_type_selector" type="select" label="Custom background">
116 <option value="bg_default" selected="True">Default Background</option>
117 <option value="bg_user">Background in your History</option>
118 </param>
119 <when value="bg_default">
120 <!--do nothing here-->
121 </when>
122 <when value="bg_user">
123 <param name="bfile" type="data" label="-bfile: Background File" />
124 </when>
125 </conditional>
126 <!--nmeme-->
127 <param name="nmeme" type="integer" value="-1" label="-nmeme: limit of sequences to pass to MEME; -1: Default behaviour" />
128 <!--ccut-->
129 <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" />
130 <!--tine-->
131 <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" />
132 <!--desc-->
133 <param name="desc" type="text" value="Galaxy MEME-Chip" label="-desc: Description of the analysis" >
134 <sanitizer>
135 <valid initial="string.printable">
136 <remove value="&apos;"/>
137 </valid>
138 <mapping initial="none">
139 <add source="&apos;" target=""/>
140 </mapping>
141 </sanitizer>
142 </param>
143 <!--MEME options-->
144 <param name="meme_mod" type="select" label="-meme-mod: Sites used in a single sequence" >
145 <option value="" selected="True"/>
146 <option value="oops" />
147 <option value="zoops" />
148 <option value="anr" />
149 </param>
150 <param name="meme_minw" type="integer" value="-1" label="-meme-minw: minimum motif width; -1: Default behaviour" />
151 <param name="meme_maxw" type="integer" value="-1" label="-meme-maxw: maximum motif width; -1: Default behaviour" />
152 <param name="meme_nmotifs" type="integer" value="-1" label="-meme-nmotifs: maximum number of motifs to find; -1: Default behaviour" />
153 <param name="meme_minsites" type="integer" value="-1" label="-meme-minsites: minimum number of sites per motif; -1: Default behaviour" />
154 <param name="meme_maxsites" type="integer" value="-1" label="-meme-maxsites: maximum number of sites per motif; -1: Default behaviour" />
155 <param name="meme_pal" type="boolean" label="-meme-pal: look for palindromes only" />
156 <!--DREME options-->
157 <param name="dreme_e" type="float" value="-1" label="-dreme-e: stop searching after reaching this E-value threshold; -1: Default behaviour" />
158 <param name="dreme_m" type="integer" value="-1" label="-dreme-e: stop searching after finding this many motifs; -1: Default behaviour" />
159 <!--CentriMo options-->
160 <param name="centrimo_score" type="float" value="-1" label="-centrimo-score: set the minimum allowed match score; -1: Default behaviour" />
161 <param name="centrimo_maxreg" type="integer" value="-1" label="-centrimo-maxreg: set the maximum region size to be considered; -1: Default behaviour" />
162 <param name="centrimo_ethresh" type="float" value="-1" label="-centrimo-ethresh: set the E-value threshold for reporting; -1: Default behaviour" />
163 <param name="centrimo_noseq" type="boolean" label="-centrimo-noseq: don't store sequence IDs in the output" />
164
165 </when>
166 </conditional>
167 </inputs>
168 <outputs>
169 <!--<data format="html" name="html_outfile" label="index" />-->
170 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
171 <data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />
172 </outputs>
173
174
175 <tests>
176 <test>
177 <param name="input_file" value="extract_genomic_dna.fa" />
178 <output name="html_file" file="sample_output.html" ftype="html" />
179 </test>
180 </tests>
181
182 <help>
183
184 .. class:: infomark
185
186 After the job finishes, save the zip file, unzip and open "index.html"
187
188 The actual meme-chip command is displayed under "Command line summary"
189
190 Defaults:
191 http://meme.nbcr.net/meme/doc/meme-chip.html
192
193 </help>
194 </tool>