Mercurial > repos > iuc > meme_dreme

annotate dreme.xml @ 0:b386032d758d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:13:22 -0400
parents
children cb8a2242bf03
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0
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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1 <tool id="meme_dreme" name="DREME" version="@WRAPPER_VERSION@.0">
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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2 <description>- Discriminative Regular Expression Motif Elicitation</description>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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3 <macros>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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4 <import>macros.xml</import>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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5 </macros>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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6 <expand macro="requirements" />
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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7 <command detect_errors="exit_code"><![CDATA[
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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8 dreme
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
iuc
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9 -o ./dreme_out
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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10 -p '$pos_fasta_file'
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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11 $norc
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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12 $alphabet_type
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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13 #if str( $neg_set_type.neg_set_type_selector ) == 'shuffle_negs':
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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14 -s '${$neg_set_type.pos_shuffle_seed}'
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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15 #elif str( $neg_set_type.neg_set_type_selector ) == 'supply_negs':
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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16 -n '${$neg_set_type.neg_fasta_file}'
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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17 #end if
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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18 #if str( $options_type.options_type_selector ) == 'advanced':
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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19 -e $options_type.e_value_thr
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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20 #if $options_type.stop_m_motifs
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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21 -m $options_type.stop_m_motifs
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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22 #end if
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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23 #if $options_type.stop_t_seconds
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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24 -t $options_type.stop_t_seconds
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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25 #end if
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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26 -g $options_type.nr_res_generalize
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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27 -mink $options_type.motif_min_k
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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28 -maxk $options_type.motif_max_k
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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29 #end if
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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30 ]]></command>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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31 <inputs>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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32 <param name="pos_fasta_file" type="data" format="fasta" label="Positive FASTA sequence file" argument="-p"
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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33 help="positive (primary) sequence file"/>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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34 <param name="alphabet_type" type="select" label="Type of sequence alphabet">
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35 <option value="-dna" selected="true">DNA (default)</option>
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36 <option value="-rna">RNA</option>
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37 <option value="-protein">Protein</option>
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38 </param>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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39 <param argument="-norc" label="Check reverse complement" type="boolean"
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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40 truevalue="" falsevalue="-norc" checked="False"
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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41 help="Search for motifs also on reverse complement strand"/>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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42 <conditional name="neg_set_type">
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43 <param name="neg_set_type_selector" type="select" label="Negative set definition">
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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44 <option value="shuffle_negs" selected="true">Shuffle positive sequences</option>
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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45 <option value="supply_negs">Supply negative sequences</option>
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46 </param>
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47 <when value="shuffle_negs">
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48 <param name="pos_shuffle_seed" type="integer" value="1"
b386032d758d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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49 label="Seed for shuffling positive sequences" argument="-s"
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50 help="(default: 1)"/>
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51 </when>
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52 <when value="supply_negs">
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53 <param name="neg_fasta_file" type="data" format="fasta"
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54 label="Negative FASTA sequence file" argument="-n"
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55 help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/>
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56 </when>
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57 </conditional>
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58 <conditional name="options_type">
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59 <param name="options_type_selector" type="select" label="Options Configuration">
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60 <option value="basic" selected="true">Basic</option>
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61 <option value="advanced">Advanced</option>
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62 </param>
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63 <when value="basic" />
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64 <when value="advanced">
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65 <param name="e_value_thr" type="float" value="0.05"
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66 label="stop if motif E-value > e" argument="-e"
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67 help="stop if motif E-value > given threshold (default: 0.05)">
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68 <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator>
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69 </param>
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70 <param name="motif_min_k" type="integer" value="3" min="1"
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71 label="Minimum width of core motif" argument="-mink"
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72 help="minimum width of core motif (default: 3)"/>
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73 <param name="motif_max_k" type="integer" value="8" min="1"
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74 label="Maximum width of core motif" argument="-maxk"
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75 help="maximum width of core motif (default: 8)"/>
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76 <param name="stop_m_motifs" type="integer" optional="True" min="1"
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77 label="Stop if m motifs have been output" argument="-m"
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78 help="stop if m motifs have been output (default: only stop at E-value threshold)"/>
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79 <param name="stop_t_seconds" type="integer" optional="True" min="1"
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80 label="Stop if the specified time has elapsed" argument="-t"
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81 help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/>
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82 <param name="nr_res_generalize" type="integer" value="100" min="1"
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83 label="Number of REs to generalize" argument="-g"
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84 help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/>
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85 </when>
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86 </conditional>
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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">
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88 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)" from_work_dir="dreme_out/dreme.html"/>
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93 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)" from_work_dir="dreme_out/dreme.txt"/>
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94 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)" from_work_dir="dreme_out/dreme.xml"/>
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95 </outputs>
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96 <tests>
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97 <test>
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98 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
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99 <param name="alphabet_type" value="-rna"/>
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100 <param name="norc" value="false"/>
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101 <param name="non_commercial_use" value="True"/>
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102 <output name="html_outfile" file="dreme1.html" lines_diff="16"/>
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103 <output name="txt_outfile" file="dreme1.txt" lines_diff="22"/>
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104 </test>
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105 <test>
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106 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
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107 <param name="alphabet_type" value="-rna"/>
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108 <param name="norc" value="false"/>
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109 <param name="options_type_selector" value="advanced"/>
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110 <param name="e_value_thr" value="0.00001"/>
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111 <param name="motif_min_k" value="4"/>
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112 <param name="motif_max_k" value="10"/>
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113 <param name="non_commercial_use" value="True"/>
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114 <output name="html_outfile" file="dreme2.html" lines_diff="29"/>
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115 <output name="txt_outfile" file="dreme2.txt" lines_diff="29"/>
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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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.
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120
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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).
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122
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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.
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124
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125 .. class:: infomark
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126
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127 For detailed information on DREME, click here_, or view the license_.
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128
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129 .. _here: http://meme-suite.org/doc/dreme.html
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130 .. _license: http://meme-suite.org/doc/copyright.html
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131
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132 ]]></help>
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133 <citations>
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134 <citation type="doi">10.1093/bioinformatics/btr261</citation>
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135 </citations>
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136 </tool>