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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
author iuc
date Mon, 14 Jul 2025 21:33:08 +0000
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-1:000000000000 0:7653ebd919bb
1 <tool id="meme_streme" name="STREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Simple, Thorough, Rapid, Enriched Motif Elicitation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">streme</xref>
8 </xrefs>
9 <expand macro="requirements"/>
10 <command detect_errors="exit_code"><![CDATA[
11 @CHECK_NON_COMMERCIAL_USE@
12 streme
13 -o ./streme_out
14 -p '$pos_fasta_file'
15 #if str( $alphabet_type.alphabet_type_selector ) == 'built_in':
16 -${alphabet_type.built_in_alphabet}
17 #else
18 -alph '${alphabet_type.custom_alphabet_file}'
19 #end if
20 #if str( $neg_set_type.neg_set_type_selector ) == 'shuffle_negs':
21 -s '${$neg_set_type.pos_shuffle_seed}'
22 #elif str( $neg_set_type.neg_set_type_selector ) == 'supply_negs':
23 -n '${$neg_set_type.neg_fasta_file}'
24 #end if
25 #if str( $options_type.options_type_selector ) == 'advanced':
26 -e $options_type.e_value_thr
27 #if $options_type.minw:
28 -minw $options_type.minw
29 #end if
30 #if $options_type.maxw:
31 -maxw $options_type.maxw
32 #end if
33 #if $options_type.nmotifs:
34 -nmotifs $options_type.nmotifs
35 #end if
36 #if $options_type.thresh:
37 -thresh $options_type.thresh
38 #end if
39 #if $options_type.seed:
40 -seed $options_type.seed
41 #end if
42 #if $options_type.align:
43 -align
44 #end if
45 #if $options_type.maxiter:
46 -maxiter $options_type.maxiter
47 #end if
48 #end if
49 ]]></command>
50 <inputs>
51 <param name="pos_fasta_file" argument="-p" type="data" format="fasta" label="Positive FASTA sequence file" help="Positive (primary) sequence file"/>
52 <conditional name="alphabet_type">
53 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
54 <option value="built_in" selected="true">Built-in Alphabets</option>
55 <option value="custom">Custom Alphabet File</option>
56 </param>
57 <when value="built_in">
58 <param name="built_in_alphabet" type="select" label="Select Built-in Alphabet">
59 <option value="dna" selected="true">DNA</option>
60 <option value="rna">RNA</option>
61 <option value="protein">Protein</option>
62 </param>
63 </when>
64 <when value="custom">
65 <param name="custom_alphabet_file" argument="-alph" type="data" format="txt" label="Custom Alphabet File" help="Provide a custom alphabet file. See STREME documentation for format."/>
66 </when>
67 </conditional>
68 <conditional name="neg_set_type">
69 <param name="neg_set_type_selector" type="select" label="Negative set definition">
70 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option>
71 <option value="supply_negs">Supply negative sequences</option>
72 </param>
73 <when value="shuffle_negs">
74 <param name="pos_shuffle_seed" argument="-s" type="integer" value="1" label="Seed for shuffling positive sequences" help="(default: 1)"/>
75 </when>
76 <when value="supply_negs">
77 <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)"/>
78 </when>
79 </conditional>
80 <conditional name="options_type">
81 <param name="options_type_selector" type="select" label="Options Configuration">
82 <option value="basic" selected="true">Basic</option>
83 <option value="advanced">Advanced</option>
84 </param>
85 <when value="basic"/>
86 <when value="advanced">
87 <param name="e_value_thr" argument="-e" type="float" value="0.05" label="E-value threshold" help="Stop if motif E-value &gt; threshold (default: 0.05)">
88 <validator type="expression" message="E-value must be &gt; 0.">value is not None and value &gt; 0</validator>
89 </param>
90 <param name="minw" argument="-minw" type="integer" min="1" optional="True" label="Minimum motif width" help="Minimum width of motifs to find (default: 6)"/>
91 <param name="maxw" argument="-maxw" type="integer" min="1" optional="True" label="Maximum motif width" help="Maximum width of motifs to find (default: 30)"/>
92 <param name="nmotifs" argument="-nmotifs" type="integer" min="1" optional="True" label="Number of motifs to find" help="Stop after finding this many motifs"/>
93 <param name="thresh" argument="-thresh" type="integer" min="1" optional="True" label="Significance threshold for reporting enriched motifs (p-value)" help="Default: 0.05 (or 0.05 if --evalue given in STREME)"/>
94 <param name="seed" argument="-seed" type="integer" optional="True" label="Random seed" help="Seed for random number generator (default: current time)"/>
95 <param name="align" argument="-align" type="boolean" truevalue="-align" falsevalue="" checked="False" label="Align motifs" help="Align output motifs (default: no alignment)"/>
96 <param name="maxiter" argument="-maxiter" type="integer" min="1" optional="True" label="Maximum EM iterations" help="Maximum number of EM iterations for motif refinement (default: 10)"/>
97 </when>
98 </conditional>
99 <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.">
100 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
101 </param>
102 </inputs>
103 <outputs>
104 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)" from_work_dir="streme_out/streme.html"/>
105 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)" from_work_dir="streme_out/streme.txt"/>
106 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)" from_work_dir="streme_out/streme.xml"/>
107 </outputs>
108 <tests>
109 <test expect_num_outputs="3">
110 <param name="pos_fasta_file" value="streme_input_pos.fasta" ftype="fasta"/>
111 <param name="alphabet_type|alphabet_type_selector" value="built_in"/>
112 <param name="alphabet_type|built_in_alphabet" value="dna"/>
113 <param name="neg_set_type|neg_set_type_selector" value="shuffle_negs"/>
114 <param name="neg_set_type|pos_shuffle_seed" value="1"/>
115 <param name="options_type|options_type_selector" value="basic"/>
116 <param name="non_commercial_use" value="True"/>
117 <output name="html_outfile" file="streme_output_test1.html" compare="contains"/>
118 <output name="txt_outfile" file="streme_output_test1.txt" compare="contains"/>
119 <output name="xml_outfile" file="streme_output_test1.xml" compare="contains"/>
120 </test>
121 <test expect_num_outputs="3">
122 <param name="pos_fasta_file" value="streme_input_pos.fasta" ftype="fasta"/>
123 <param name="alphabet_type|alphabet_type_selector" value="custom"/>
124 <param name="alphabet_type|custom_alphabet_file" value="alphabet.txt" ftype="txt"/>
125 <param name="neg_set_type|neg_set_type_selector" value="shuffle_negs"/>
126 <param name="neg_set_type|pos_shuffle_seed" value="1"/>
127 <param name="options_type|options_type_selector" value="advanced"/>
128 <param name="options_type|e_value_thr" value="0.01"/>
129 <param name="options_type|nmotifs" value="3"/>
130 <param name="non_commercial_use" value="True"/>
131 <output name="html_outfile" file="streme_output_test2.html" compare="contains"/>
132 <output name="txt_outfile" file="streme_output_test2.txt" compare="contains"/>
133 <output name="xml_outfile" file="streme_output_test2.xml" compare="contains"/>
134 </test>
135 <test expect_num_outputs="3">
136 <param name="pos_fasta_file" value="streme_input_pos2.fasta" ftype="fasta"/>
137 <param name="alphabet_type|alphabet_type_selector" value="built_in"/>
138 <param name="alphabet_type|built_in_alphabet" value="protein"/>
139 <param name="neg_set_type|neg_set_type_selector" value="supply_negs"/>
140 <param name="neg_set_type|neg_fasta_file" value="streme_input_neg2.fasta" ftype="fasta"/>
141 <param name="options_type|options_type_selector" value="advanced"/>
142 <param name="options_type|minw" value="5"/>
143 <param name="options_type|maxw" value="20"/>
144 <param name="non_commercial_use" value="True"/>
145 <output name="html_outfile" file="streme_output_test3.html" compare="contains"/>
146 <output name="txt_outfile" file="streme_output_test3.txt" compare="contains"/>
147 <output name="xml_outfile" file="streme_output_test3.xml" compare="contains"/>
148 </test>
149 </tests>
150 <help><![CDATA[
151 .. class:: warningmark
152
153 For detailed information on STREME, click here_, or view the license_.
154
155 .. _here: https://meme-suite.org/meme/doc/streme.html
156 .. _license: http://meme-suite.org/doc/copyright.html
157
158 ]]></help>
159 <citations>
160 <citation type="doi">10.1093/bioinformatics/btr261</citation>
161 </citations>
162 </tool>