Mercurial > repos > proteore > proteore_filter_keywords_values
annotate filter_kw_val.xml @ 1:cb9555653b09 draft
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author | proteore |
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date | Fri, 21 Sep 2018 06:03:25 -0400 |
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1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.09.21"> |
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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 to combine your filters (if more than one)" 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="text" selected="true">Enter keywords (copy/paste)</option> |
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73 <option value="file">Choose a file containing keywords</option> |
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74 </param> |
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75 <when value="None" /> |
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76 <when value="text" > |
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77 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords must be separated by ";", for example: A8K2U0;Q5TA79;O43175' > |
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78 <sanitizer> |
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79 <valid initial="string.printable"> |
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80 <remove value="'"/> |
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81 </valid> |
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82 <mapping initial="none"> |
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83 <add source="'" target="__sq__"/> |
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84 </mapping> |
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85 </sanitizer> |
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86 </param> |
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87 </when> |
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88 <when value="file" > |
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89 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" /> |
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90 </when> |
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91 </conditional> |
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92 </repeat> |
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93 <repeat name="value" title="Filter by value" > |
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94 <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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95 <conditional name="v" > |
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96 <param argument="--val" type="select" label="Filter by value" > |
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97 <option value="None">---</option> |
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98 <option value="Equal">=</option> |
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99 <option value="Higher">></option> |
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100 <option value="Equal or higher">>=</option> |
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101 <option value="Lower"><</option> |
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102 <option value="Equal or lower"><=</option> |
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103 <option value="Different">!=</option> |
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104 </param> |
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105 <when value="None" > |
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106 </when> |
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107 <when value="Equal" > |
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108 <param name="equal" type="float" value="" label="Value" /> |
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109 </when> |
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110 <when value="Higher" > |
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111 <param type="float" name="higher" value="" label="Value" /> |
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112 </when> |
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113 <when value="Equal or higher" > |
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114 <param type="float" name="equal_higher" value="" label="Value" /> |
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115 </when> |
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116 <when value="Lower" > |
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117 <param type="float" name="lower" value="" label="Value" /> |
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118 </when> |
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119 <when value="Equal or lower" > |
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120 <param type="float" name="equal_lower" value="" label="Value" /> |
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121 </when> |
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122 <when value="Different"> |
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123 <param type="float" name="different" value="" label="Value"/> |
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124 </when> |
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125 </conditional> |
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126 </repeat> |
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127 <repeat name="values_range" title="Filter by range of values"> |
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128 <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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129 <param name="bottom_value" type="float" value="" label="Please enter the bottom value" /> |
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130 <param name="top_value" type="float" value="" label="Please enter the top value" /> |
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131 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" /> |
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132 </repeat> |
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133 </inputs> |
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134 <outputs> |
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135 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" /> |
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136 <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" /> |
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137 </outputs> |
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138 <tests> |
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139 <test> |
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140 <param name="input1" value="Lacombe_et_al_2017_OK.txt" /> |
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141 <param name="header" value="true" /> |
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142 <param name="operator" value="OR"/> |
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143 <param name="sort_column" value="c1"/> |
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144 <param name="reversed_sort" value="false"/> |
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145 <repeat name="keyword"> |
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146 <param name="ncol" value="c1" /> |
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147 <param name="match" value="True" /> |
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148 <conditional name="k"> |
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149 <param name="kw" value="text" /> |
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150 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" /> |
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151 </conditional> |
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152 </repeat> |
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153 <repeat name="value"> |
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154 <param name="ncol" value="c3"/> |
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155 <conditional name="v"> |
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156 <param name="val" value="Higher"/> |
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157 <param name="higher" value="20" /> |
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158 </conditional> |
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159 </repeat> |
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160 <output name="output1" file="output.csv" /> |
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161 <output name="filtered_file" file="filtered_output.csv" /> |
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162 </test> |
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163 </tests> |
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164 <help><![CDATA[ |
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165 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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166 |
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167 **Filter by keyword(s)** |
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168 |
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169 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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170 |
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171 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 |
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172 |
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173 - If you choose to upload a file in a text format in which each line is a keyword, for example: |
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174 |
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175 REV |
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176 |
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177 TRYP_PIG |
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178 |
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179 ALDOA_RABBIT |
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180 |
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181 **The line that contains these keywords will be eliminated from input file.** |
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182 |
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183 **Keywords search can be applied by performing either exact match or partial one by using the following option** |
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184 |
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185 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. |
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186 |
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187 - If you choose **No**, all the fields containing the keyword will be removed. |
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188 |
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189 For example: |
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190 |
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191 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. |
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192 |
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193 **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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194 |
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195 ----- |
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196 |
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197 **Filter by values** |
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198 |
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199 You can filter your data by a column of numerical values. |
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200 Enter the column to be use and select one operator in the list : |
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201 |
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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 Then enter the value to filter and specify the column to apply that option. |
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210 If a row contains a value that correspond to your settings, it will be filtered. |
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211 |
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212 ----- |
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213 |
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214 **Filter by a range of values** |
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215 |
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216 You can also set a range of values to filter your file. |
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217 In opposition to value filter, rows with values inside of the defined range are kept. |
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218 |
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219 Rows with values outside of the defined range will be filtered. |
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220 |
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221 ----- |
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222 |
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223 **AND/OR operator** |
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224 |
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225 Since you can add as many filters as you want, you can choose how filters apply on your data. |
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226 |
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227 AND or OR operator option works on all filters : |
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228 |
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229 - OR : only one filter to be satisfied to remove one row |
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230 - AND : all filters must be satisfied to remove one row |
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231 |
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232 ----- |
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233 |
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234 **Sort the results files** |
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235 |
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236 You can sort the result file if you wish, it can help you to check results. |
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237 |
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238 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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239 |
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240 Rows stay intact, just in different order like excel. |
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241 You can also choose ascending or descending order, by default ascending order is set. |
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242 |
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243 ----- |
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244 |
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245 **Output** |
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246 |
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247 The tool will produce 2 output files. |
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248 |
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249 * A text file containing the resulting filtered input file. |
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250 |
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251 * A text file containing the rows removed from the input file. |
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252 |
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253 ----- |
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254 |
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255 .. class:: infomark |
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256 |
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257 **Authors** |
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258 |
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259 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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260 |
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261 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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262 |
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263 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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264 |
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265 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
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266 |
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267 ]]></help> |
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268 <citations> |
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269 </citations> |
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270 </tool> |