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comparison meme_chip-06a47bbf8b4e/meme_chip_wrapper.xml @ 0:0814784ad7de draft

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Uploaded v1.0.0 from testtoolshed
author kevyin
date Tue, 06 Nov 2012 22:51:20 -0500
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1 <tool id="meme_chip_wrapper" name="meme-chip" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="4.9.0">meme-chip</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&gt;&amp;1 || echo "Error running MEME."
82 <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}-->
83 <!--&amp;&amp; zip -r result $html_outfile.files_path-->
84 &amp;&amp; cd ${memechip_out.files_path}
85 &amp;&amp; zip -rp memechip_out ./
86 &amp;&amp; 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="&apos;"/>
131 </valid>
132 <mapping initial="none">
133 <add source="&apos;" 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="${tool.name} on ${on_string}" />
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>