Mercurial > repos > iuc > meme_dreme

comparison dreme.xml @ 0:315f05ef7d49 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:12:03 -0400
parents
children a154fa30afd1
comparison
equal deleted inserted replaced
-1:000000000000 0:315f05ef7d49
1 <tool id="meme_dreme" name="DREME" version="@WRAPPER_VERSION@.0">
2 <description>- Discriminative Regular Expression Motif Elicitation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 dreme
9 -o ./dreme_out
10 -p '$pos_fasta_file'
11 $norc
12 $alphabet_type
13 #if str( $neg_set_type.neg_set_type_selector ) == 'shuffle_negs':
14 -s '${$neg_set_type.pos_shuffle_seed}'
15 #elif str( $neg_set_type.neg_set_type_selector ) == 'supply_negs':
16 -n '${$neg_set_type.neg_fasta_file}'
17 #end if
18 #if str( $options_type.options_type_selector ) == 'advanced':
19 -e $options_type.e_value_thr
20 #if $options_type.stop_m_motifs
21 -m $options_type.stop_m_motifs
22 #end if
23 #if $options_type.stop_t_seconds
24 -t $options_type.stop_t_seconds
25 #end if
26 -g $options_type.nr_res_generalize
27 -mink $options_type.motif_min_k
28 -maxk $options_type.motif_max_k
29 #end if
30 ]]></command>
31 <inputs>
32 <param name="pos_fasta_file" type="data" format="fasta" label="Positive FASTA sequence file" argument="-p"
33 help="positive (primary) sequence file"/>
34 <param name="alphabet_type" type="select" label="Type of sequence alphabet">
35 <option value="-dna" selected="true">DNA (default)</option>
36 <option value="-rna">RNA</option>
37 <option value="-protein">Protein</option>
38 </param>
39 <param argument="-norc" label="Check reverse complement" type="boolean"
40 truevalue="" falsevalue="-norc" checked="False"
41 help="Search for motifs also on reverse complement strand"/>
42 <conditional name="neg_set_type">
43 <param name="neg_set_type_selector" type="select" label="Negative set definition">
44 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option>
45 <option value="supply_negs">Supply negative sequences</option>
46 </param>
47 <when value="shuffle_negs">
48 <param name="pos_shuffle_seed" type="integer" value="1"
49 label="Seed for shuffling positive sequences" argument="-s"
50 help="(default: 1)"/>
51 </when>
52 <when value="supply_negs">
53 <param name="neg_fasta_file" type="data" format="fasta"
54 label="Negative FASTA sequence file" argument="-n"
55 help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
56 </when>
57 </conditional>
58 <conditional name="options_type">
59 <param name="options_type_selector" type="select" label="Options Configuration">
60 <option value="basic" selected="true">Basic</option>
61 <option value="advanced">Advanced</option>
62 </param>
63 <when value="basic" />
64 <when value="advanced">
65 <param name="e_value_thr" type="float" value="0.05"
66 label="stop if motif E-value > e" argument="-e"
67 help="stop if motif E-value > given threshold (default: 0.05)">
68 <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator>
69 </param>
70 <param name="motif_min_k" type="integer" value="3" min="1"
71 label="Minimum width of core motif" argument="-mink"
72 help="minimum width of core motif (default: 3)"/>
73 <param name="motif_max_k" type="integer" value="8" min="1"
74 label="Maximum width of core motif" argument="-maxk"
75 help="maximum width of core motif (default: 8)"/>
76 <param name="stop_m_motifs" type="integer" optional="True" min="1"
77 label="Stop if m motifs have been output" argument="-m"
78 help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
79 <param name="stop_t_seconds" type="integer" optional="True" min="1"
80 label="Stop if the specified time has elapsed" argument="-t"
81 help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
82 <param name="nr_res_generalize" type="integer" value="100" min="1"
83 label="Number of REs to generalize" argument="-g"
84 help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
85 </when>
86 </conditional>
87 <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">
88 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
89 </param>
90 </inputs>
91 <outputs>
92 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)" from_work_dir="dreme_out/dreme.html"/>
93 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)" from_work_dir="dreme_out/dreme.txt"/>
94 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)" from_work_dir="dreme_out/dreme.xml"/>
95 </outputs>
96 <tests>
97 <test>
98 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
99 <param name="alphabet_type" value="-rna"/>
100 <param name="norc" value="false"/>
101 <param name="non_commercial_use" value="True"/>
102 <output name="html_outfile" file="dreme1.html" lines_diff="16"/>
103 <output name="txt_outfile" file="dreme1.txt" lines_diff="22"/>
104 </test>
105 <test>
106 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
107 <param name="alphabet_type" value="-rna"/>
108 <param name="norc" value="false"/>
109 <param name="options_type_selector" value="advanced"/>
110 <param name="e_value_thr" value="0.00001"/>
111 <param name="motif_min_k" value="4"/>
112 <param name="motif_max_k" value="10"/>
113 <param name="non_commercial_use" value="True"/>
114 <output name="html_outfile" file="dreme2.html" lines_diff="29"/>
115 <output name="txt_outfile" file="dreme2.txt" lines_diff="29"/>
116 </test>
117 </tests>
118 <help><![CDATA[
119 DREME (Discriminative Regular Expression Motif Elicitation) discovers short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in your sequences compared with shuffled sequences or given control sequences.
120
121 DREME finds relatively short motifs (up to 8 positions) fast. The input to DREME is one or two sets of sequences. The control (-n parameter) sequences should be approximately the same length as the primary (-p parameter) sequences. If you do not provide a control set, the program shuffles the primary set to provide a control set. The program uses Fisher's Exact Test to determine significance of each motif found in the postive set as compared with its representation in the control set, using a significance threshold that may be set (-e parameter).
122
123 DREME achieves its high speed by restricting its search to regular expressions based on the IUPAC alphabet representing bases and ambiguous characters, and by using a heuristic estimate of generalised motifs' statistical significance.
124
125 .. class:: infomark
126
127 For detailed information on DREME, click here_, or view the license_.
128
129 .. _here: http://meme-suite.org/doc/dreme.html
130 .. _license: http://meme-suite.org/doc/copyright.html
131
132 ]]></help>
133 <citations>
134 <citation type="doi">10.1093/bioinformatics/btr261</citation>
135 </citations>
136 </tool>