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comparison meme_chip.xml @ 7:c321ab02c2a0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
author iuc
date Fri, 20 Apr 2018 09:03:24 -0400
parents 444093446b0b
children 81c0806236ef
comparison
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6:444093446b0b 7:c321ab02c2a0
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <code file="get_meme_motif_databases.py" /> 7 <code file="get_meme_motif_databases.py" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import os 9 #import os
10 #set primary_output = $os.path.join($output.files_path, "index.html") 10 #set primary_output = $os.path.join($output.files_path, "index.html")
11 #set options_type = $options_type_cond.options_type
12 meme-chip '$input' 11 meme-chip '$input'
13 -noecho 12 -noecho
14 #if $control: 13 #if $control:
15 -neg '$control' 14 -neg '$control'
16 #end if 15 #end if
17 $sequence_alphabet 16 $sequence_alphabet
18 -o '$output.files_path' 17 -o '$output.files_path'
19 #if str($options_type)=='advanced': 18 #if str($options_type_cond.options_type)=='advanced':
20 ## FIXME: CentriMo cannot be run, See the comments in the input section. 19 ## FIXME: CentriMo cannot be run, See the comments in the input section.
21 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo 20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
22 ## #if str($run_centrimo) == "yes": 21 ## #if str($run_centrimo) == "yes":
23 ## -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
24 ## #if $options_type_cond.run_centrimo_cond.centrimo_local: 23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local:
38 ## #end if 37 ## #end if
39 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip: 38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip:
40 ## -centrimo-flip 39 ## -centrimo-flip
41 ## #end if 40 ## #end if
42 ## #end if 41 ## #end if
43 #if $options_type_cond.search_given_strand: 42 $options_type_cond.search_given_strand
44 -norc
45 #end if
46 -order $options_type_cond.background_model_order 43 -order $options_type_cond.background_model_order
47 #if str($options_type_cond.subsampling_cond.subsampling) == "no": 44 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
48 -norand 45 -norand
49 #set seed = $options_type_cond.subsampling_cond.subsampling.seed 46 #if $options_type_cond.subsampling_cond.subsampling.seed:
50 #if $seed:
51 -seed $options_type_cond.subsampling_cond.subsampling.seed 47 -seed $options_type_cond.subsampling_cond.subsampling.seed
52 #end if 48 #end if
53 #end if 49 #end if
54 #if $options_type_cond.nmeme: 50 #if $options_type_cond.nmeme:
55 -nmeme $options_type_cond.nmeme 51 -nmeme $options_type_cond.nmeme
56 #end if 52 #end if
57 #if $options_type_cond.ccut: 53 #if $options_type_cond.ccut:
58 -ccut $options_type_cond.ccut 54 -ccut $options_type_cond.ccut
59 #end if 55 #end if
60 -group-thresh $options_type_cond.group_threash 56 -group-thresh $options_type_cond.group_threash
61 #if $options_type_cond.group_weak: 57 #if str($options_type_cond.group_weak):
62 -group-weak $options_type_cond.group_weak 58 -group-weak $options_type_cond.group_weak
63 #end if 59 #end if
64 -filter-thresh $options_type_cond.filter_thresh 60 -filter-thresh $options_type_cond.filter_thresh
65 #if $options_type_cond.old_clustering: 61 $options_type_cond.old_clustering
66 -old-clustering
67 #end if
68 -meme-mod $options_type_cond.meme_mod 62 -meme-mod $options_type_cond.meme_mod
69 #if $options_type_cond.meme_minw: 63 #if $options_type_cond.meme_minw:
70 -meme-minw $options_type_cond.meme_minw 64 -meme-minw $options_type_cond.meme_minw
71 #end if 65 #end if
72 #if $options_type_cond.meme_maxw: 66 #if $options_type_cond.meme_maxw:
79 -meme-minsites $options_type_cond.meme_minsites 73 -meme-minsites $options_type_cond.meme_minsites
80 #end if 74 #end if
81 #if $options_type_cond.meme_maxsites: 75 #if $options_type_cond.meme_maxsites:
82 -meme-maxsites $options_type_cond.meme_maxsites 76 -meme-maxsites $options_type_cond.meme_maxsites
83 #end if 77 #end if
84 #if $options_type_cond.meme_pal: 78 $options_type_cond.meme_pal
85 -meme-pal
86 #end if
87 -dreme-e $options_type_cond.dreme_e 79 -dreme-e $options_type_cond.dreme_e
88 -dreme-m $options_type_cond.dreme_m 80 -dreme-m $options_type_cond.dreme_m
89 -spamo-skip 81 -spamo-skip
90 -fimo-skip 82 -fimo-skip
91 #end if 83 #end if
143 <option value="1" selected="True">1st order model of sequences</option> 135 <option value="1" selected="True">1st order model of sequences</option>
144 <option value="2">2nd order model of sequences</option> 136 <option value="2">2nd order model of sequences</option>
145 <option value="3">3rd order model of sequences</option> 137 <option value="3">3rd order model of sequences</option>
146 <option value="4">4th order model of sequences</option> 138 <option value="4">4th order model of sequences</option>
147 </param> 139 </param>
148 <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"/> 140 <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/>
149 <conditional name="subsampling_cond"> 141 <conditional name="subsampling_cond">
150 <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)"> 142 <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)">
151 <option value="yes" selected="true">Yes</option> 143 <option value="yes" selected="true">Yes</option>
152 <option value="no">No</option> 144 <option value="no">No</option>
153 </param> 145 </param>
154 <when value="yes"> 146 <when value="yes">
155 <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"/> 147 <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/>
156 </when> 148 </when>
157 <when value="no"/> 149 <when value="no"/>
158 </conditional> 150 </conditional>
159 <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"/> 151 <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"/>
160 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" /> 152 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
161 <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"/> 153 <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"/>
162 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/> 154 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
163 <param name="search_given_strand" type="boolean" truevalue="true" falsevalue="" checked="False" label="Search given strand only"/> 155 <param name="search_given_strand" type="boolean" truevalue="-norc" falsevalue="" checked="False" label="Search given strand only"/>
164 <param name="old_clustering" type="boolean" truevalue="true" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/> 156 <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
165 <param name="meme_mod" type="select" label="What is the expected motif site distribution?"> 157 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
166 <option value="oops" selected="True">One occurance per sequence</option> 158 <option value="oops" selected="True">One occurance per sequence</option>
167 <option value="zoops">Zero or one occurances per sequence</option> 159 <option value="zoops">Zero or one occurances per sequence</option>
168 <option value="anr">Any number of repititions</option> 160 <option value="anr">Any number of repititions</option>
169 </param> 161 </param>
170 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/> 162 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/>
171 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/> 163 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/>
172 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/> 164 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/>
173 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/> 165 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/>
174 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/> 166 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/>
175 <param name="meme_pal" type="boolean" truevalue="true" falsevalue="" checked="False" label="Look for palindromes only"/> 167 <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/>
176 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/> 168 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
177 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" /> 169 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
178 </when> 170 </when>
179 </conditional> 171 </conditional>
180 <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"> 172 <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">