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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
author iuc
date Thu, 29 Aug 2024 10:18:52 +0000
parents 441cbb2068c0
children
comparison
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5:441cbb2068c0 6:6b2cad4d63b3
1 <tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Discriminative Regular Expression Motif Elicitation</description> 2 <description>- Discriminative Regular Expression Motif Elicitation</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements"/>
7 <requirement type="package" version="2.7">python</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
10 @CHECK_NON_COMMERCIAL_USE@ 8 @CHECK_NON_COMMERCIAL_USE@
11 dreme 9 dreme
12 -o ./dreme_out 10 -o ./dreme_out
13 -p '$pos_fasta_file' 11 -p '$pos_fasta_file'
30 -mink $options_type.motif_min_k 28 -mink $options_type.motif_min_k
31 -maxk $options_type.motif_max_k 29 -maxk $options_type.motif_max_k
32 #end if 30 #end if
33 ]]></command> 31 ]]></command>
34 <inputs> 32 <inputs>
35 <param name="pos_fasta_file" type="data" format="fasta" label="Positive FASTA sequence file" argument="-p" 33 <param name="pos_fasta_file" argument="-p" type="data" format="fasta" label="Positive FASTA sequence file" help="positive (primary) sequence file"/>
36 help="positive (primary) sequence file"/>
37 <param name="alphabet_type" type="select" label="Type of sequence alphabet"> 34 <param name="alphabet_type" type="select" label="Type of sequence alphabet">
38 <option value="-dna" selected="true">DNA (default)</option> 35 <option value="-dna" selected="true">DNA (default)</option>
39 <option value="-rna">RNA</option> 36 <option value="-rna">RNA</option>
40 <option value="-protein">Protein</option> 37 <option value="-protein">Protein</option>
41 </param> 38 </param>
42 <param argument="-norc" label="Check reverse complement" type="boolean" 39 <param argument="-norc" type="boolean" truevalue="" falsevalue="-norc" checked="False" label="Check reverse complement" help="Search for motifs also on reverse complement strand"/>
43 truevalue="" falsevalue="-norc" checked="False"
44 help="Search for motifs also on reverse complement strand"/>
45 <conditional name="neg_set_type"> 40 <conditional name="neg_set_type">
46 <param name="neg_set_type_selector" type="select" label="Negative set definition"> 41 <param name="neg_set_type_selector" type="select" label="Negative set definition">
47 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option> 42 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option>
48 <option value="supply_negs">Supply negative sequences</option> 43 <option value="supply_negs">Supply negative sequences</option>
49 </param> 44 </param>
50 <when value="shuffle_negs"> 45 <when value="shuffle_negs">
51 <param name="pos_shuffle_seed" type="integer" value="1" 46 <param name="pos_shuffle_seed" argument="-s" type="integer" value="1" label="Seed for shuffling positive sequences" help="(default: 1)"/>
52 label="Seed for shuffling positive sequences" argument="-s"
53 help="(default: 1)"/>
54 </when> 47 </when>
55 <when value="supply_negs"> 48 <when value="supply_negs">
56 <param name="neg_fasta_file" type="data" format="fasta" 49 <param name="neg_fasta_file" argument="-n" type="data" format="fasta" label="Negative FASTA sequence file" help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
57 label="Negative FASTA sequence file" argument="-n"
58 help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
59 </when> 50 </when>
60 </conditional> 51 </conditional>
61 <conditional name="options_type"> 52 <conditional name="options_type">
62 <param name="options_type_selector" type="select" label="Options Configuration"> 53 <param name="options_type_selector" type="select" label="Options Configuration">
63 <option value="basic" selected="true">Basic</option> 54 <option value="basic" selected="true">Basic</option>
64 <option value="advanced">Advanced</option> 55 <option value="advanced">Advanced</option>
65 </param> 56 </param>
66 <when value="basic" /> 57 <when value="basic"/>
67 <when value="advanced"> 58 <when value="advanced">
68 <param name="e_value_thr" type="float" value="0.05" 59 <param name="e_value_thr" argument="-e" type="float" value="0.05" label="stop if motif E-value &gt; e" help="stop if motif E-value &gt; given threshold (default: 0.05)">
69 label="stop if motif E-value > e" argument="-e" 60 <validator type="expression" message="Set e-value must be &gt; 0.">value is not None and value &gt; 0</validator>
70 help="stop if motif E-value > given threshold (default: 0.05)">
71 <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator>
72 </param> 61 </param>
73 <param name="motif_min_k" type="integer" value="3" min="1" 62 <param name="motif_min_k" argument="-mink" type="integer" min="1" value="3" label="Minimum width of core motif" help="minimum width of core motif (default: 3)"/>
74 label="Minimum width of core motif" argument="-mink" 63 <param name="motif_max_k" argument="-maxk" type="integer" min="1" value="8" label="Maximum width of core motif" help="maximum width of core motif (default: 8)"/>
75 help="minimum width of core motif (default: 3)"/> 64 <param name="stop_m_motifs" argument="-m" type="integer" min="1" optional="True" label="Stop if m motifs have been output" help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
76 <param name="motif_max_k" type="integer" value="8" min="1" 65 <param name="stop_t_seconds" argument="-t" type="integer" min="1" optional="True" label="Stop if the specified time has elapsed" help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
77 label="Maximum width of core motif" argument="-maxk" 66 <param name="nr_res_generalize" argument="-g" type="integer" min="1" value="100" label="Number of REs to generalize" help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
78 help="maximum width of core motif (default: 8)"/>
79 <param name="stop_m_motifs" type="integer" optional="True" min="1"
80 label="Stop if m motifs have been output" argument="-m"
81 help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
82 <param name="stop_t_seconds" type="integer" optional="True" min="1"
83 label="Stop if the specified time has elapsed" argument="-t"
84 help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
85 <param name="nr_res_generalize" type="integer" value="100" min="1"
86 label="Number of REs to generalize" argument="-g"
87 help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
88 </when> 67 </when>
89 </conditional> 68 </conditional>
90 <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"> 69 <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
91 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 70 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
92 </param> 71 </param>
93 </inputs> 72 </inputs>
94 <outputs> 73 <outputs>
95 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)" from_work_dir="dreme_out/dreme.html"/> 74 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)" from_work_dir="dreme_out/dreme.html"/>
100 <test> 79 <test>
101 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/> 80 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
102 <param name="alphabet_type" value="-rna"/> 81 <param name="alphabet_type" value="-rna"/>
103 <param name="norc" value="false"/> 82 <param name="norc" value="false"/>
104 <param name="non_commercial_use" value="True"/> 83 <param name="non_commercial_use" value="True"/>
105 <output name="html_outfile" file="dreme_output_test1.html" compare="contains"/> 84 <output name="html_outfile">
106 <output name="txt_outfile" file="dreme_output_test1.txt" compare="contains"/> 85 <assert_contents>
107 <output name="xml_outfile" file="dreme_output_test1.xml" compare="contains"/> 86 <has_text text="pvalue"/>
87 <has_text text="UUUUCC"/>
88 <has_text text="evalue"/>
89 <has_text text="matches"/>
90 <has_text text="DREME"/>
91 </assert_contents>
92 </output>
93 <output name="txt_outfile">
94 <assert_contents>
95 <has_text text="RNA-LIKE"/>
96 <has_text text="shuffled"/>
97 <has_text text="0.221"/>
98 <has_text text="DREME"/>
99 <has_text text="letter-probability matrix"/>
100 <has_n_lines n="84"/>
101 </assert_contents>
102 </output>
103 <output name="xml_outfile">
104 <assert_contents>
105 <has_text text="Adenine"/>
106 <has_text text="command_line"/>
107 <has_text text="Uracil"/>
108 <has_text text="DREME"/>
109 <has_text text="evalue"/>
110 </assert_contents>
111 </output>
108 </test> 112 </test>
109 <test> 113 <test>
110 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/> 114 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
111 <param name="alphabet_type" value="-rna"/> 115 <param name="alphabet_type" value="-rna"/>
112 <param name="norc" value="false"/> 116 <param name="norc" value="false"/>
113 <param name="options_type_selector" value="advanced"/> 117 <param name="options_type_selector" value="advanced"/>
114 <param name="e_value_thr" value="0.00001"/> 118 <param name="e_value_thr" value="0.00001"/>
115 <param name="motif_min_k" value="4"/> 119 <param name="motif_min_k" value="4"/>
116 <param name="motif_max_k" value="10"/> 120 <param name="motif_max_k" value="10"/>
117 <param name="non_commercial_use" value="True"/> 121 <param name="non_commercial_use" value="True"/>
118 <output name="html_outfile" file="dreme_output_test2.html" compare="contains"/> 122 <output name="html_outfile">
119 <output name="txt_outfile" file="dreme_output_test2.txt" compare="contains"/> 123 <assert_contents>
120 <output name="xml_outfile" file="dreme_output_test2.xml" compare="contains"/> 124 <has_text text="shuffled positive sequences"/>
125 <has_text text="UUCUCU"/>
126 <has_text text="YAGG"/>
127 <has_text text="runtime"/>
128 <has_text text="DREME"/>
129 <has_text text="ACGU"/>
130 </assert_contents>
131 </output>
132 <output name="txt_outfile">
133 <assert_contents>
134 <has_text text="RNA-LIKE"/>
135 <has_text text="from shuffled positives"/>
136 <has_text text="MOTIF UUYUCY DREME"/>
137 <has_text text="probability"/>
138 <has_text text="YAGG"/>
139 <has_n_lines n="68"/>
140 </assert_contents>
141 </output>
142 <output name="xml_outfile">
143 <assert_contents>
144 <has_text text="Purine"/>
145 <has_text text="1000"/>
146 <has_text text="shuffled"/>
147 <has_text text="rna"/>
148 <has_text text="evalue"/>
149 </assert_contents>
150 </output>
121 </test> 151 </test>
122 </tests> 152 </tests>
123 <help><![CDATA[ 153 <help><![CDATA[
124 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. 154 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.
125 155