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comparison meme_chip.xml @ 6:444093446b0b draft

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Uploaded
author iuc
date Mon, 16 Apr 2018 13:01:45 -0400
parents ff7dc6057652
children c321ab02c2a0
comparison
equal deleted inserted replaced
5:ff7dc6057652 6:444093446b0b
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 11 #set options_type = $options_type_cond.options_type
12 meme-chip '$input' 12 meme-chip '$input'
13 -noecho 13 -noecho
14 #if str($control): 14 #if $control:
15 -neg '$control' 15 -neg '$control'
16 #end if 16 #end if
17 $sequence_alphabet
17 -o '$output.files_path' 18 -o '$output.files_path'
18 #if str($options_type)=='advanced': 19 #if str($options_type)=='advanced':
19 ## FIXME: CentriMo cannot be run, See the comments in the input section. 20 ## FIXME: CentriMo cannot be run, See the comments in the input section.
20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo 21 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
21 ## #if str($run_centrimo) == "yes": 22 ## #if str($run_centrimo) == "yes":
22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path 23 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
23 ## #if str($options_type_cond.run_centrimo_cond.centrimo_local): 24 ## #if $options_type_cond.run_centrimo_cond.centrimo_local:
24 ## -centrimo-local 25 ## -centrimo-local
25 ## #end if 26 ## #end if
26 ## #if str($options_type_cond.run_centrimo_cond.centrimo_score): 27 ## #if $options_type_cond.run_centrimo_cond.centrimo_score:
27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score 28 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
28 ## #end if 29 ## #end if
29 ## #if str($options_type_cond.run_centrimo_cond.centrimo_maxreg): 30 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg 31 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
31 ## #end if 32 ## #end if
32 ## #if str($options_type_cond.run_centrimo_cond.centrimo_ethresh): 33 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh 34 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
34 ## #end if 35 ## #end if
35 ## #if str($options_type_cond.run_centrimo_cond.centrimo_noseq): 36 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
36 ## -centrimo-noseq 37 ## -centrimo-noseq
37 ## #end if 38 ## #end if
38 ## #if str($options_type_cond.run_centrimo_cond.centrimo_flip): 39 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip:
39 ## -centrimo-flip 40 ## -centrimo-flip
40 ## #end if 41 ## #end if
41 ## #end if 42 ## #end if
42 #if str($options_type_cond.search_given_strand): 43 #if $options_type_cond.search_given_strand:
43 -norc 44 -norc
44 #end if 45 #end if
45 -order $options_type_cond.background_model_order 46 -order $options_type_cond.background_model_order
46 #if str($options_type_cond.subsampling_cond.subsampling) == "no": 47 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
47 -norand 48 -norand
48 #set seed = $options_type_cond.subsampling_cond.subsampling.seed 49 #set seed = $options_type_cond.subsampling_cond.subsampling.seed
49 #if str($seed): 50 #if $seed:
50 -seed $options_type_cond.subsampling_cond.subsampling.seed 51 -seed $options_type_cond.subsampling_cond.subsampling.seed
51 #end if 52 #end if
52 #end if 53 #end if
53 #if str($options_type_cond.nmeme): 54 #if $options_type_cond.nmeme:
54 -nmeme $options_type_cond.nmeme 55 -nmeme $options_type_cond.nmeme
55 #end if 56 #end if
56 #if str($options_type_cond.ccut): 57 #if $options_type_cond.ccut:
57 -ccut $options_type_cond.ccut 58 -ccut $options_type_cond.ccut
58 #end if 59 #end if
59 -group-thresh $options_type_cond.group_threash 60 -group-thresh $options_type_cond.group_threash
60 #if str($options_type_cond.group_weak): 61 #if $options_type_cond.group_weak:
61 -group-weak $options_type_cond.group_weak 62 -group-weak $options_type_cond.group_weak
62 #end if 63 #end if
63 -filter-thresh $options_type_cond.filter_thresh 64 -filter-thresh $options_type_cond.filter_thresh
64 #if str($options_type_cond.old_clustering): 65 #if $options_type_cond.old_clustering:
65 -old-clustering 66 -old-clustering
66 #end if 67 #end if
67 -meme-mod $options_type_cond.meme_mod 68 -meme-mod $options_type_cond.meme_mod
68 #if str($options_type_cond.meme_minw): 69 #if $options_type_cond.meme_minw:
69 -meme-minw $options_type_cond.meme_minw 70 -meme-minw $options_type_cond.meme_minw
70 #end if 71 #end if
71 #if str($options_type_cond.meme_maxw): 72 #if $options_type_cond.meme_maxw:
72 -meme-maxw $options_type_cond.meme_maxw 73 -meme-maxw $options_type_cond.meme_maxw
73 #end if 74 #end if
74 #if str($options_type_cond.meme_nmotifs): 75 #if $options_type_cond.meme_nmotifs:
75 -meme-nmotifs $options_type_cond.meme_nmotifs 76 -meme-nmotifs $options_type_cond.meme_nmotifs
76 #end if 77 #end if
77 #if str($options_type_cond.meme_minsites): 78 #if $options_type_cond.meme_minsites:
78 -meme-minsites $options_type_cond.meme_minsites 79 -meme-minsites $options_type_cond.meme_minsites
79 #end if 80 #end if
80 #if str($options_type_cond.meme_maxsites): 81 #if $options_type_cond.meme_maxsites:
81 -meme-maxsites $options_type_cond.meme_maxsites 82 -meme-maxsites $options_type_cond.meme_maxsites
82 #end if 83 #end if
83 #if str($options_type_cond.meme_pal): 84 #if $options_type_cond.meme_pal:
84 -meme-pal 85 -meme-pal
85 #end if 86 #end if
86 -dreme-e $options_type_cond.dreme_e 87 -dreme-e $options_type_cond.dreme_e
87 -dreme-m $options_type_cond.dreme_m 88 -dreme-m $options_type_cond.dreme_m
88 -spamo-skip 89 -spamo-skip
189 <param name="non_commercial_use" value="True"/> 190 <param name="non_commercial_use" value="True"/>
190 <output name="output" file="output1.html" ftype="html" compare="contains"/> 191 <output name="output" file="output1.html" ftype="html" compare="contains"/>
191 </test> 192 </test>
192 <test> 193 <test>
193 <param name="input" value="input1.fasta" ftype="fasta"/> 194 <param name="input" value="input1.fasta" ftype="fasta"/>
194 <param name="sequence_alphabet" value="rna"/> 195 <param name="sequence_alphabet" value="-rna"/>
195 <param name="options_type" value="advanced"/> 196 <param name="options_type" value="advanced"/>
196 <param name="background_model_order" value="0"/> 197 <param name="background_model_order" value="0"/>
197 <param name="non_commercial_use" value="True"/> 198 <param name="non_commercial_use" value="True"/>
198 <output name="output" file="output1.html" ftype="html" compare="contains"/> 199 <output name="output" file="output1.html" ftype="html" compare="contains"/>
199 </test> 200 </test>