Mercurial > repos > proteore > proteore_filter_keywords_values

annotate filter_kw_val.xml @ 0:a55e8b137c6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Wed, 19 Sep 2018 05:01:15 -0400
parents
children cb9555653b09
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.08.22">
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2 <description></description>
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3 <requirements>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command><![CDATA[
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9 python $__tool_directory__/filter_kw_val.py
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10 -i "$input1,$header"
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11 -o "$output1"
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12 --filtered_file "$filtered_file"
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13 --operator "$operator"
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14
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15 ## Keywords
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16 #for $key in $keyword
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17 #if $key.k.kw != "None"
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18 #if $key.k.kw == "text"
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19 --kw "$key.k.txt" "$key.ncol" "$key.match"
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20 #else if $key.k.kw == "file"
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21 --kw_file "$key.k.file" "$key.ncol" "$key.match"
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22 #end if
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23 #end if
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24 #end for
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25
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26 ## value to filter
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27 #for $val in $value
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28 #if $val.v.val != "None"
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29 --value
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30 #if $val.v.val == "Equal"
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31 $val.v.equal "$val.ncol" "="
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32 #else if $val.v.val == "Higher"
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33 $val.v.higher "$val.ncol" ">"
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34 #else if $val.v.val == "Equal or higher"
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35 $val.v.equal_higher "$val.ncol" ">="
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36 #else if $val.v.val == "Lower"
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37 $val.v.lower "$val.ncol" "<"
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38 #else if $val.v.val == "Equal or lower"
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39 $val.v.equal_lower "$val.ncol" "<="
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40 #else
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41 $val.v.different "$val.ncol" "!="
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42 #end if
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43 #end if
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44 #end for
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45
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46 ##range of values to keep
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47 #for $vr in $values_range
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48 #if vr
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49 --values_range $vr.bottom_value $vr.top_value $vr.ncol $vr.inclusive
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50 #end if
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51 #end for
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52
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53 #if $sort_column != ""
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54 --sort_col "$sort_column,$reversed_sort"
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55 #end if
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56
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57 ]]></command>
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58 <inputs>
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59 <param type="data" name="input1" format="txt,tabular" label="Input file" help="Input file is a tab-delimited file containing proteomics identification and/or quantitative results" />
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60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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61 <param name="operator" type="select" label="Please select an operator for your filters" help="OR : only one filter must be satisfied to filter a row, AND : all your filters must be satisfied to filter a row" >
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62 <option value="OR" selected="True">OR</option>
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63 <option value="AND">AND</option>
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64 </param>
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65 <param name="sort_column" type="text" value="" label="If you want to sort the result files by values from a column, please enter a column number" help="For example : fill in 'c1' if you want to sort your result file by the column 1 values." />
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66 <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>
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67 <repeat name="keyword" title="Filter by keywords" >
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68 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
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69 <param type="boolean" name="match" truevalue="True" label="Would you like to search for exact match?" help='Choosing "Yes" will only filter out exact match (i.e. case sensitive), see below for more details' />
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70 <conditional name="k" >
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71 <param argument="--kw" type="select" label="Filter by keyword" >
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72 <option value="None" selected="True">---</option>
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73 <option value="text">Enter keywords (copy/paste)</option>
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74 <option value="file">Choose a file containing keywords</option>
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75 </param>
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76 <when value="None" />
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77 <when value="text" >
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78 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' >
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79 <sanitizer>
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80 <valid initial="string.printable">
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81 <remove value="&apos;"/>
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82 </valid>
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83 <mapping initial="none">
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84 <add source="&apos;" target="__sq__"/>
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85 </mapping>
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86 </sanitizer>
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87 </param>
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88 </when>
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89 <when value="file" >
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90 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
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91 </when>
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92 </conditional>
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93 </repeat>
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94 <repeat name="value" title="Filter by value" >
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95 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
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96 <conditional name="v" >
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97 <param argument="--val" type="select" label="Filter by value" >
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98 <option value="None">---</option>
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99 <option value="Equal">=</option>
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100 <option value="Higher">&gt;</option>
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101 <option value="Equal or higher">&gt;=</option>
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102 <option value="Lower">&lt;</option>
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103 <option value="Equal or lower">&lt;=</option>
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104 <option value="Different">!=</option>
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105 </param>
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106 <when value="None" >
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107 </when>
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108 <when value="Equal" >
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109 <param name="equal" type="float" value="" label="Value" />
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110 </when>
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111 <when value="Higher" >
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112 <param type="float" name="higher" value="" label="Value" />
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113 </when>
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114 <when value="Equal or higher" >
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115 <param type="float" name="equal_higher" value="" label="Value" />
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116 </when>
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117 <when value="Lower" >
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118 <param type="float" name="lower" value="" label="Value" />
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119 </when>
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120 <when value="Equal or lower" >
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121 <param type="float" name="equal_lower" value="" label="Value" />
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122 </when>
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123 <when value="Different">
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124 <param type="float" name="different" value="" label="Value"/>
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125 </when>
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126 </conditional>
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127 </repeat>
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128 <repeat name="values_range" title="Filter by range of values">
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129 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
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130 <param name="bottom_value" type="float" value="" label="Please enter the bottom value" />
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131 <param name="top_value" type="float" value="" label="Please enter the top value" />
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132 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
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133 </repeat>
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134 </inputs>
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135 <outputs>
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136 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
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137 <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" />
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138 </outputs>
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139 <tests>
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140 <test>
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141 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
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142 <param name="header" value="true" />
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143 <param name="operator" value="OR"/>
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144 <param name="sort_column" value="c1"/>
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145 <param name="reversed_sort" value="false"/>
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146 <repeat name="keyword">
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147 <param name="ncol" value="c1" />
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148 <param name="match" value="True" />
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149 <conditional name="k">
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150 <param name="kw" value="text" />
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151 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" />
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152 </conditional>
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153 </repeat>
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154 <repeat name="value">
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155 <param name="ncol" value="c3"/>
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156 <conditional name="v">
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157 <param name="val" value="Higher"/>
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158 <param name="higher" value="20" />
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159 </conditional>
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160 </repeat>
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161 <output name="output1" file="output.csv" />
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162 <output name="filtered_file" file="filtered_output.csv" />
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163 </test>
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164 </tests>
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165 <help><![CDATA[
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166 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output).
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167
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168 **Filter by keyword(s)**
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169
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170 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords.
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171
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172 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
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173
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174 - If you choose to upload a file in a text format in which each line is a keyword, for example:
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175
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176 REV
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177
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178 TRYP_PIG
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179
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180 ALDOA_RABBIT
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181
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182 **The line that contains these keywords will be eliminated from input file.**
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183
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184 **Keywords search can be applied by performing either exact match or partial one by using the following option**
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185
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186 - If you choose **Yes**, only the fields that contains exactly the same content will be removed.
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187
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188 - If you choose **No**, all the fields containing the keyword will be removed.
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189
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190 For example:
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191
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192 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
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193
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194 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed.
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195
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196 -----
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197
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198 **Filter by values**
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199
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200 You can filter your data by a column of numerical values.
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201 Enter the column to be use and select one operator in the list :
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202
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203 - =
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204 - !=
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205 - <
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206 - <=
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207 - >
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208 - >=
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209
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210 Then enter the value to filter and specify the column to apply that option.
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211 If a row contains a value that correspond to your settings, it will be filtered.
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212
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213 -----
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214
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215 **Filter by a range of values**
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216
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217 You can also set a range of values to filter your file.
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218 In opposition to value filter, rows with values inside of the defined range are kept.
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219
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220 Rows with values outside of the defined range will be filtered.
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221
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222 -----
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223
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224 **AND/OR operator**
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225
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226 Since you can add as many filters as you want, you can choose how filters apply on your data.
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227
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228 AND or OR operator option works on all filters :
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229
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230 - OR : only one filter to be satisfied to remove one row
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231 - AND : all filters must be satisfied to remove one row
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232
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233 -----
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234
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235 **Sort the results files**
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236
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237 You can sort the result file if you wish, it can help you to check results.
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238
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239 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
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240
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241 Rows stay intact, just in different order like excel.
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242 You can also choose ascending or descending order, by default ascending order is set.
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243
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244 -----
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245
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246 **Output**
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247
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248 The tool will produce 2 output files.
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249
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250 * A text file containing the resulting filtered input file.
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251
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252 * A text file containing the rows removed from the input file.
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253
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254 -----
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255
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256 .. class:: infomark
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257
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258 **Authors**
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259
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260 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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261
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262 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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263
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264 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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265
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266 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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267
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268 ]]></help>
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269 <citations>
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270 </citations>
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271 </tool>