Mercurial > repos > proteore > proteore_filter_keywords_values

annotate filter_kw_val.xml @ 3:68cee865018e 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, 16 Jan 2019 08:30:53 -0500
parents 52a7afd01c6d
children 2080e2a4f209
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="MQoutputfilter" name="Filter by keywords and/or numerical value" version="2019.01.16">
0
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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" "$key.k.header" "$key.k.ncol" "$key.ncol" "$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>
2
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59 <param type="data" name="input1" format="txt,tabular" label="Input file" />
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60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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61 <param name="operator" type="select" label="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>
2
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65
0
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66 <repeat name="keyword" title="Filter by keywords" >
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67 <param name="ncol" type="text" value="c1" label="Column number on which 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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68 <param type="boolean" name="match" truevalue="True" label="Search for exact match?" help='Choosing "Yes" will only filter out exact match (e.g. case sensitive), see help section' />
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69 <conditional name="k" >
2
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70 <param name="kw" type="select" label="Enter keywords" >
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71 <option value="text" selected="true">copy/paste</option>
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72 <option value="file">File containing keywords</option>
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73 </param>
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74 <when value="text" >
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75 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords must be separated by tab, space or carriage return into the form field, for example: A8K2U0 Q5TA79 O43175' >
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76 <sanitizer>
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77 <valid initial="string.printable">
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78 <remove value="&apos;"/>
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79 </valid>
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80 <mapping initial="none">
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81 <add source="&apos;" target="__sq__"/>
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82 </mapping>
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83 </sanitizer>
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84 </param>
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85 </when>
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86 <when value="file" >
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87 <param name="file" type="data" format="txt,tabular" label="File containing keywords" />
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88 <param name="ncol" type="text" value="c1" label="Specify the column containing keywords" help='For example, fill in "c1" if keywords are in the first column' />
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89 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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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 numerical value" >
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94 <param name="ncol" type="text" value="c1" label="Column number on which to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
0
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95 <conditional name="v" >
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96 <param name="val" type="select" label="Select operator" >
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97 <option value="Equal">=</option>
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98 <option value="Higher">&gt;</option>
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99 <option value="Equal or higher">&gt;=</option>
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100 <option value="Lower">&lt;</option>
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101 <option value="Equal or lower">&lt;=</option>
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102 <option value="Different">!=</option>
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103 </param>
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104 <when value="Equal" >
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105 <param name="equal" type="float" value="" label="Value" />
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106 </when>
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107 <when value="Higher" >
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108 <param type="float" name="higher" value="" label="Value" />
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109 </when>
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110 <when value="Equal or higher" >
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111 <param type="float" name="equal_higher" value="" label="Value" />
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112 </when>
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113 <when value="Lower" >
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114 <param type="float" name="lower" value="" label="Value" />
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115 </when>
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116 <when value="Equal or lower" >
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117 <param type="float" name="equal_lower" value="" label="Value" />
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118 </when>
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119 <when value="Different">
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120 <param type="float" name="different" value="" label="Value"/>
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121 </when>
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122 </conditional>
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123 </repeat>
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124 <repeat name="values_range" title="Filter by range of numerical values">
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125 <param name="ncol" type="text" value="c1" label="Column number on which 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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126 <param name="bottom_value" type="float" value="" label="Enter the bottom value" />
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127 <param name="top_value" type="float" value="" label="Enter the top value" />
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128 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
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129 </repeat>
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130 <param name="sort_column" type="text" value="" label="Sort result files by:" help="Fill in 'c1' if you want to sort your result file by the column 1 values" />
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131 <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>
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132 </inputs>
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133 <outputs>
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134 <data name="output1" format="tsv" label="${tool.name} on ${input1.name}" />
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135 <data name="filtered_file" format="tsv" label="${tool.name} on ${input1.name} - Filtered lines" />
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136 </outputs>
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137 <tests>
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138 <test>
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139 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
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140 <param name="header" value="true" />
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141 <param name="operator" value="OR"/>
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142 <param name="sort_column" value="c1"/>
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143 <param name="reversed_sort" value="false"/>
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144 <repeat name="keyword">
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145 <param name="ncol" value="c1" />
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146 <param name="match" value="True" />
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147 <conditional name="k">
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148 <param name="kw" value="text" />
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149 <param name="txt" value="P04264 P35908 P13645 Q5D862 Q5T749 Q8IW75 P81605 P22531 P59666 P78386" />
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150 </conditional>
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151 </repeat>
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152 <repeat name="value">
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153 <param name="ncol" value="c3"/>
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154 <conditional name="v">
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155 <param name="val" value="Higher"/>
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156 <param name="higher" value="20" />
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157 </conditional>
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158 </repeat>
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159 <output name="output1" file="output.csv" />
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160 <output name="filtered_file" file="filtered_output.csv" />
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161 </test>
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162 </tests>
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163 <help><![CDATA[
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164 **Description**
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165
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166 This tool allows to filter out data according to different criteria such as keywords (e.g. a list of contaminants) or numerical values (e.g. intensity measurements below a given threshold).
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167 A boolean operator "OR/AND" allows to combine different type of filters making this tool very powerful.
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168
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169 -----
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170
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171 **Input**
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172
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173 A table (file in txt, tab, tsv, csv format) of your identification and/or quantification results for example.
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174
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175 -----
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176
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177 **Parameters**
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178
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179 **AND/OR operator**
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180
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181 As many filters as needed can be combined, you can choose how filters apply on your data by using the following boolean operators:
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182
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183 - OR: only one filter must be satisfied to remove one row
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184 - AND: all filters must be satisfied to remove one row
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185
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186 -----
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187
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188 **Filter by keyword(s)**
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189
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190 Click on the "Filter by keywords" box to use it. You can either fill in the field (copy/paste) or upload a file which contains the keywords.
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191
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192 "Column number on which to apply the filter": You must then specify the column number of your input file on wich to apply the filter by keywords.
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193
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194 - If you choose to fill in the field, the keywords should be separated by tab, space or carriage return into the form field, for example: A8K2U0 Q5TA79 O43175
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195
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196 - If you choose to upload a file in a text format in which each line is a keyword, for example:
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197
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198 TRYP_PIG
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199
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200 ALDOA_RABBIT
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201
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202 LYSO_ECOLI
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203
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204 Lines that contains these keywords will be removed from input file.
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205
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206 "Search for exact match?": Keywords search can be applied by performing either exact match or partial one by using the following option:
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207
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208 - If you choose **Yes**, only the fields that contains exactly the same content will be removed.
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209
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210 - If you choose **No**, all the fields containing the keyword will be removed.
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211
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212 Example:
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213
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214 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly the word "kinase" will be removed.
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215
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216 **No** option (partial match) for "kinase": lines which contain "kinase" and lines with "alpha-kinase" (and so on) will be removed.
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217
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218 -----
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219
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220 **Filter by numerical values**: You can filter your data by a column of numerical values.
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221
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222 "Column number on which to apply the filter": you must specify the column number of your input file on wich to apply the filter by numerical value.
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223
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224 Then select one of the operators in the list :
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225
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226 - = (equal)
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227 - != (not equal)
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228 - < (lower than)
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229 - <= (lower than or equal to)
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230 - > (greater than)
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231 - >= (greater than or equal to)
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232
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233 Then enter the numerical threshold to apply by filling the "Value" box.
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234 If you choose > 10, each row containing a numerical value (in the chosen column of your input file) that correspond to your settings will be filtered out.
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235
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236 -----
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237
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238 **Filter by a range of values**: You can also set a range of values to filter your file.
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239 Conversely to the numeric filter, rows with numerical values within the defined range will be kept while rows with values out of this range will be filtered out.
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240
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241 -----
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242
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243 **Sort results files**
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244
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245 You can sort your results by column in ascending (default value) or descending by entering the column number on which to sort the data.
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246
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247 -----
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248
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249 **Output**
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250
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251 The tool returns two output files.
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252
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253 * A text file containing the results that pass your filters
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254
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255 * A text file containing the rows removed from the input file (i.e. containing data taht do not pass your filter(s).
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256
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257 -----
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258
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259 .. class:: infomark
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260
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261 **Authors**
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262
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263 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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264
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265 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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266
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267 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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268
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269 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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270
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271 ]]></help>
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272 <citations>
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273 </citations>
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274 </tool>