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comparison meme_chip.xml @ 8:81c0806236ef draft

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author iuc
date Thu, 12 Jul 2018 08:48:01 -0400
parents c321ab02c2a0
children 4fc125833bc2
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7:c321ab02c2a0 8:81c0806236ef
14 -neg '$control' 14 -neg '$control'
15 #end if 15 #end if
16 $sequence_alphabet 16 $sequence_alphabet
17 -o '$output.files_path' 17 -o '$output.files_path'
18 #if str($options_type_cond.options_type)=='advanced': 18 #if str($options_type_cond.options_type)=='advanced':
19 ## FIXME: CentriMo cannot be run, See the comments in the input section. 19 #if str($options_type_cond.run_centrimo_cond.run_centrimo) == "yes":
20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo 20 -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
21 ## #if str($run_centrimo) == "yes": 21 #if $options_type_cond.run_centrimo_cond.centrimo_local:
22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path 22 -centrimo-local
23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local: 23 #end if
24 ## -centrimo-local 24 #if $options_type_cond.run_centrimo_cond.centrimo_score:
25 ## #end if 25 -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
26 ## #if $options_type_cond.run_centrimo_cond.centrimo_score: 26 #end if
27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score 27 #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
28 ## #end if 28 -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
29 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg: 29 #end if
30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg 30 #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
31 ## #end if 31 -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
32 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh: 32 #end if
33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh 33 #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
34 ## #end if 34 -centrimo-noseq
35 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq: 35 #end if
36 ## -centrimo-noseq 36 #if $options_type_cond.run_centrimo_cond.centrimo_flip:
37 ## #end if 37 -centrimo-flip
38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip: 38 #end if
39 ## -centrimo-flip 39 #end if
40 ## #end if
41 ## #end if
42 $options_type_cond.search_given_strand 40 $options_type_cond.search_given_strand
43 -order $options_type_cond.background_model_order 41 -order $options_type_cond.background_model_order
44 #if str($options_type_cond.subsampling_cond.subsampling) == "no": 42 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
45 -norand 43 -norand
46 #if $options_type_cond.subsampling_cond.subsampling.seed: 44 #if $options_type_cond.subsampling_cond.subsampling.seed:
96 <option value="basic" selected="true">Basic</option> 94 <option value="basic" selected="true">Basic</option>
97 <option value="advanced">Advanced</option> 95 <option value="advanced">Advanced</option>
98 </param> 96 </param>
99 <when value="basic"/> 97 <when value="basic"/>
100 <when value="advanced"> 98 <when value="advanced">
101 <!--
102 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
103 <conditional name="run_centrimo_cond"> 99 <conditional name="run_centrimo_cond">
104 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?"> 100 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
105 <option value="yes" selected="true">Yes</option> 101 <option value="yes" selected="true">Yes</option>
106 <option value="no">No</option> 102 <option value="no">No</option>
107 </param> 103 </param>
108 <when value="yes"> 104 <when value="yes">
109
110 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
111 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
112 select list is changed. This composition used to work (see Examples->Dynamic Options section of
113 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in
114 the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
115
116 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True"> 105 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
117 <options from_data_table="meme_motif_databases"> 106 <options from_data_table="meme_motif_databases">
107 <column name="name" index="1"/>
108 <column name="value" index="2"/>
118 <filter type="sort_by" column="1"/> 109 <filter type="sort_by" column="1"/>
119 <validator type="no_options" message="No MEME motif databases are available for the selected input"/> 110 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
120 </options> 111 </options>
121 </param> 112 </param>
122 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/> 113 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/>
127 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/> 118 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
128 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/> 119 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
129 </when> 120 </when>
130 <when value="no"/> 121 <when value="no"/>
131 </conditional> 122 </conditional>
132 -->
133 <param name="background_model_order" type="select" label="Select the order of the Markov background model"> 123 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
134 <option value="0">0-order model of sequences</option> 124 <option value="0">0-order model of sequences</option>
135 <option value="1" selected="True">1st order model of sequences</option> 125 <option value="1" selected="True">1st order model of sequences</option>
136 <option value="2">2nd order model of sequences</option> 126 <option value="2">2nd order model of sequences</option>
137 <option value="3">3rd order model of sequences</option> 127 <option value="3">3rd order model of sequences</option>