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1 <tool id="meme_fimo" name="FIMO" version="0.0.1">
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2 <requirements><requirement type="package">meme</requirement></requirements>
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3 <description>- Find Individual Motif Occurrences</description>
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4 <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
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5
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6 #if str( $options_type.options_type_selector ) == 'advanced':
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7 --max-seq-length "${options_type.max_seq_length}"
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8 --max-stored-scores "${options_type.max_stored_scores }"
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9 --motif-pseudo "${options_type.motif_pseudo}"
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10 ${options_type.norc}
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11 --output-pthresh "${options_type.output_pthresh}"
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12
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13
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14 #for $motif in $options_type.motifs:
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15 --motif "${motif.motif}"
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16 #end for
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17
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18 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
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19 --bgfile "motif-file"
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20 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
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21 --bgfile "${options_type.bgfile_type.bgfile}"
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22 #end if
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23
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24 #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
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25 --no-qvalue
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26 #else:
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27 --output-qthresh "${options_type.qvalue_type.output_qthresh}"
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28 #end if
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29 #end if
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30
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31 "${input_motifs}"
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32
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33 #if str( $fasta_type.fasta_type_selector ) == 'history':
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34 "${fasta_type.input_database}"
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35 #else:
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36 "${fasta_type.input_database.fields.path}"
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37 #end if
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38
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39 '
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40
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41 '${html_outfile.files_path}'
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42
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43 '${html_outfile}'
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44
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45 '${interval_outfile}'
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46
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47 '${txt_outfile}'
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48
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49 '${xml_outfile}'
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50
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51 '${gff_outfile}'
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52
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53 </command>
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54 <inputs>
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55 <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
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56
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57 <conditional name="fasta_type">
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58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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59 <option value="cached">Locally Cached sequences</option>
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60 <option value="history" selected="true">Sequences from your history</option>
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61 </param>
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62 <when value="cached">
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63 <param name="input_database" type="select" label="Genome to search">
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64 <options from_data_table="all_fasta">
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65 </options>
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66 </param>
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67 </when>
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68 <when value="history">
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69 <param format="fasta" name="input_database" type="data" label="Sequences"/>
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70 </when>
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71 </conditional>
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72
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73 <conditional name="options_type">
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74 <param name="options_type_selector" type="select" label="Options Configuration">
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75 <option value="basic" selected="true">Basic</option>
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76 <option value="advanced">Advanced</option>
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77 </param>
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78 <when value="basic">
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79 <!-- do nothing here -->
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80 </when>
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81 <when value="advanced">
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82
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83 <conditional name="bgfile_type">
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84 <param name="bgfile_type_selector" type="select" label="Background file type">
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85 <option value="motif-file">Use Frequencies from Motif File</option>
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86 <option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
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87 <option value="bgfile">Use Frequencies from Background File</option>
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88 </param>
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89 <when value="motif-file">
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90 <!-- do nothing here -->
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91 </when>
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92 <when value="default">
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93 <!-- do nothing here -->
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94 </when>
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95 <when value="bgfile">
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96 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
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97 </when>
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98 </conditional>
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99
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100 <repeat name="motifs" title="Limit to specified motif">
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101 <param name="motif" type="text" value="" label="Specify motif by id" />
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102 </repeat>
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103
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104 <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
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105 <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
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106 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
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107 <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
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108 <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
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109
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110 <conditional name="qvalue_type">
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111 <param name="qvalue_type_selector" type="select" label="q-value options">
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112 <option value="no-qvalue">Do not compute q-value</option>
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113 <option value="q-value" selected="true">Compute q-value</option>
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114 </param>
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115 <when value="no-qvalue">
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116 <!-- do nothing here -->
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117 </when>
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118 <when value="q-value">
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119 <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
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120 </when>
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121 </conditional>
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122
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123 </when>
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124 </conditional>
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125
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126 <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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127 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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128 </param>
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129
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130 </inputs>
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131 <outputs>
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132 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
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133 <actions>
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134 <conditional name="fasta_type.fasta_type_selector">
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135 <when value="cached">
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136 <action type="metadata" name="dbkey">
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137 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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138 <filter type="param_value" column="0" value="seq" keep="True"/>
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139 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
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140 </option>
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141 </action>
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142 </when>
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143 </conditional>
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144 </actions>
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145 </data>
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146 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
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147 <actions>
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148 <conditional name="fasta_type.fasta_type_selector">
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149 <when value="cached">
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150 <action type="metadata" name="dbkey">
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151 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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152 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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153 </option>
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154 </action>
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155 </when>
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156 </conditional>
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157 </actions>
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158 </data>
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159 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
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160 <actions>
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161 <conditional name="fasta_type.fasta_type_selector">
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162 <when value="cached">
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163 <action type="metadata" name="dbkey">
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164 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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165 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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166 </option>
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167 </action>
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168 </when>
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169 </conditional>
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170 </actions>
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171 </data>
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172 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
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173 <actions>
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174 <conditional name="fasta_type.fasta_type_selector">
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175 <when value="cached">
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176 <action type="metadata" name="dbkey">
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177 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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178 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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179 </option>
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180 </action>
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181 </when>
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182 </conditional>
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183 </actions>
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184 </data>
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185 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
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186 <actions>
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187 <conditional name="fasta_type.fasta_type_selector">
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188 <when value="cached">
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189 <action type="metadata" name="dbkey">
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190 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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191 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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192 </option>
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193 </action>
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194 </when>
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195 </conditional>
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196 </actions>
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197 </data>
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198 </outputs>
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199 <tests>
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200 <test>
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201 <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
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202 <param name="fasta_type_selector" value="history"/>
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203 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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204 <param name="options_type_selector" value="basic"/>
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205 <param name="non_commercial_use" value="True"/>
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206 <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
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207 <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
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208 <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
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209 <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
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210 <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
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211 </test>
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212 </tests>
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213 <help>
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214
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215 .. class:: warningmark
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216
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217 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
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218
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219 .. class:: infomark
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220
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221 **To cite FIMO:**
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222 `Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. <http://www.ncbi.nlm.nih.gov/pubmed/21330290>`_
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223
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224
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225 For detailed information on FIMO, click here_. To view the license_.
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226
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227 ------
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228
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229 **Citation**
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230
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231 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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232
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233
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234 .. _here: http://meme.nbcr.net/meme/fimo-intro.html
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235 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
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236
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237 </help>
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238 </tool>
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