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1 <tool id="meme_chip_wrapper" name="meme-chip" version="1.2.5">
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2 <requirements>
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4
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3 <requirement type="package" version="4.8.0">meme</requirement>
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4 <requirement type="package" version="2.6">perl_module_HTML_Template</requirement>
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5 </requirements>
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6 <description></description>
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2
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7 <version_command>echo "MEME version r4.10.0"</version_command>
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9
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8 <command> meme-chip $input_file -o ${html_outfile.files_path}
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8
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9 -db $__tool_directory__/JASPAR_CORE_2016.meme
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10 #if str( $options_type.options_type_selector ) == 'advanced':
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11 #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
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12 -bfile "${ str( $options_type.bg_type.bfile ) }"
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13 #end if
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14
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15 #if str( $options_type.ccut ) != '-1':
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16 -ccut "${ str( $options_type.ccut ) }"
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17 #end if
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18
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19 #if str( $options_type.time ) != '-1':
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20 -time "${ str( $options_type.time ) }"
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21 #end if
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22
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23 -desc "${ str( $options_type.desc ) }"
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24
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25 #if str( $options_type.meme_mod ) != '':
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26 -meme-mod "${ str($options_type.meme_mod) }"
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27 #end if
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28
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29 #if str( $options_type.meme_minw ) != '-1':
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30 -meme-minw "${ str($options_type.meme_minw) }"
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31 #end if
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32
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33 #if str( $options_type.meme_maxw ) != '-1':
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34 -meme-maxw "${ str($options_type.meme_maxw) }"
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35 #end if
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36
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37 #if str( $options_type.meme_nmotifs ) != '-1':
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38 -meme-nmotifs "${ str($options_type.meme_nmotifs) }"
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39 #end if
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40
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41 #if str( $options_type.meme_minsites ) != '-1':
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42 -meme-minsites "${ str($options_type.meme_minsites) }"
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43 #end if
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44
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45 #if str( $options_type.meme_maxsites ) != '-1':
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46 -meme-maxsites "${ str($options_type.meme_maxsites) }"
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47 #end if
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48
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49 #if $options_type.meme_pal:
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50 -meme-pal "${ str($options_type.meme_pal) }"
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51 #end if
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52
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53 #if str( $options_type.dreme_e ) != '-1.0':
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54 -dreme-e "${ str($options_type.dreme_e) }"
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55 #end if
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56
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57 #if str( $options_type.dreme_m ) != '-1':
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58 -dreme-m "${ str($options_type.dreme_m) }"
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59 #end if
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60
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61 #if str($options_type.centrimo_score) != '-1.0':
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62 -centrimo-score "${ str($options_type.centrimo_score) }"
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63 #end if
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64
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65 #if str( $options_type.centrimo_maxreg ) != '-1':
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66 -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }"
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67 #end if
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68
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69 #if str( $options_type.centrimo_ethresh ) != '-1.0':
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70 -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }"
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71 #end if
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72
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73 #if $options_type.centrimo_noseq:
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74 -centrimo-noseq
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75 #end if
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76
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77 #end if
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78 <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
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79 2>&1 || echo "Error running MEME."
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80 && mv ${html_outfile.files_path}/index.html ${html_outfile}
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81 && zip -r result $html_outfile.files_path
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82 <!--&& cd ${memechip_out.files_path}
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83 && zip -rp memechip_out ./
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84 && mv memechip_out.zip ${memechip_out}-->
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85 </command>
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86 <inputs>
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87 <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
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88 <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases">
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89 <options from_data_table="meme_chip_motifs">
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90 <filter type="sort_by" column="1"/>
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91 <validator type="no_options" message="No indexes are available for the selected dataset"/>
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92 </options>
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93
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94 </param>
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95 <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="True">
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96 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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97 </param>
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98 <conditional name="options_type">
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99 <param name="options_type_selector" type="select" label="Options Configuration">
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100 <option value="basic" selected="true">Basic</option>
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101 <option value="advanced">Advanced</option>
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102 </param>
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103 <when value="basic">
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104 <!-- do nothing here -->
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105 </when>
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106 <when value="advanced">
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107 <!--bfile-->
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108 <conditional name="bg_type">
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109 <param name="bg_type_selector" type="select" label="Custom background">
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110 <option value="bg_default" selected="True">Default Background</option>
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111 <option value="bg_user">Background in your History</option>
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112 </param>
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113 <when value="bg_default">
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114 <!--do nothing here-->
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115 </when>
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116 <when value="bg_user">
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117 <param name="bfile" type="data" label="-bfile: Background File" />
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118 </when>
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119 </conditional>
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120 <!--ccut-->
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121 <param name="ccut" type="integer" value="-1" label="-ccut: Max size of a seq before it is cut down; 0: do not cut; -1: Default behaviour" />
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122 <!--tine-->
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123 <param name="time" type="integer" value="-1" label="-time: Maximum time (minutes) that this program has to run and create output in; -1: no limit" />
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124 <!--desc-->
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125 <param name="desc" type="text" value="Galaxy MEME-Chip" label="-desc: Description of the analysis" >
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126 <sanitizer>
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127 <valid initial="string.printable">
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128 <remove value="'"/>
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129 </valid>
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130 <mapping initial="none">
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131 <add source="'" target=""/>
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132 </mapping>
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133 </sanitizer>
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134 </param>
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135 <!--MEME options-->
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136 <param name="meme_mod" type="select" label="-meme-mod: Sites used in a single sequence" >
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137 <option value="" selected="True"/>
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138 <option value="oops" />
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139 <option value="zoops" />
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140 <option value="anr" />
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141 </param>
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142 <param name="meme_minw" type="integer" value="-1" label="-meme-minw: minimum motif width; -1: Default behaviour" />
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143 <param name="meme_maxw" type="integer" value="-1" label="-meme-maxw: maximum motif width; -1: Default behaviour" />
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144 <param name="meme_nmotifs" type="integer" value="-1" label="-meme-nmotifs: maximum number of motifs to find; -1: Default behaviour" />
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145 <param name="meme_minsites" type="integer" value="-1" label="-meme-minsites: minimum number of sites per motif; -1: Default behaviour" />
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146 <param name="meme_maxsites" type="integer" value="-1" label="-meme-maxsites: maximum number of sites per motif; -1: Default behaviour" />
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147 <param name="meme_pal" type="boolean" label="-meme-pal: look for palindromes only" />
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148 <!--DREME options-->
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149 <param name="dreme_e" type="float" value="-1" label="-dreme-e: stop searching after reaching this E-value threshold; -1: Default behaviour" />
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150 <param name="dreme_m" type="integer" value="-1" label="-dreme-e: stop searching after finding this many motifs; -1: Default behaviour" />
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151 <!--CentriMo options-->
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152 <param name="centrimo_score" type="float" value="-1" label="-centrimo-score: set the minimum allowed match score; -1: Default behaviour" />
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153 <param name="centrimo_maxreg" type="integer" value="-1" label="-centrimo-maxreg: set the maximum region size to be considered; -1: Default behaviour" />
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154 <param name="centrimo_ethresh" type="float" value="-1" label="-centrimo-ethresh: set the E-value threshold for reporting; -1: Default behaviour" />
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155 <param name="centrimo_noseq" type="boolean" label="-centrimo-noseq: don't store sequence IDs in the output" />
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156
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157 </when>
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158 </conditional>
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159 </inputs>
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160 <outputs>
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161 <data format="html" name="html_outfile" label="index" />
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162 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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163 <!--<data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />-->
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164 </outputs>
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165
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166
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167 <tests>
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168 <test>
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169 <param name="input_file" value="extract_genomic_dna.fa" />
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170 <output name="html_file" file="sample_output.html" ftype="html" />
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171 </test>
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172 </tests>
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173
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174 <help>
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175
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176 .. class:: infomark
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177
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178 After the job finishes, save the zip file, unzip and open "index.html"
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179
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180 The actual meme-chip command is displayed under "Command line summary"
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181
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182 Defaults:
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183 http://meme.nbcr.net/meme/doc/meme-chip.html
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184
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185 </help>
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186 </tool>
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