Mercurial > repos > iuc > meme_streme

annotate streme.xml @ 0:7653ebd919bb draft default tip

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