Mercurial > repos > proteore > filter_keywords_values

annotate filter_kw_val.xml @ 0:6a45ccfc0e4c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Sun, 26 Nov 2017 18:36:43 -0500
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children d29e469b6b20
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="MQoutputfilter" name="Filter out keywords and/or numerical values" version="0.1.0">
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2 <description>Filter a file by keywords or values</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 --trash_file "$trash_file"
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13
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14 ## Keywords
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15 #for $i, $key in enumerate($keyword)
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16 #if $key.k.kw != "None"
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17 #if $key.k.kw == "text"
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18 --kw "$key.k.txt" "$key.k.ncol" "$key.match"
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19 #else if $key.k.kw == "file"
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20 --kw_file "$key.k.file" "$key.k.ncol" "$key.match"
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21 #end if
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22 #end if
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23 #end for
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24
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25 ## Number of proteins
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26 #for $i, $val in enumerate($value)
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27 #if $val.v.val != "None"
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28 --value
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29 #if $val.v.val == "Equal"
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30 $val.v.equal "$value.ncol" "="
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31 #else if $val.v.val == "Higher"
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32 $val.v.higher "$val.v.ncol" ">"
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33 #else if $val.v.val == "Equal or higher"
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34 $val.v.equal_higher "$val.v.ncol" ">="
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35 #else if $val.v.val == "Lower"
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36 $val.v.lower "$val.v.ncol" "<"
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37 #else
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38 $val.v.equal_lower "$val.v.ncol" "<="
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39 #end if
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40 #end if
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41 #end for
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42
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43 ]]></command>
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44 <inputs>
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45 <param type="data" name="input1" format="txt,tabular" label="Input file" help="Input file is a tab-delimited file containing proteomics results (e.g. output file from MaxQuant or Proline softwares" />
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46 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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47 <repeat name="keyword" title="Filter by keywords" >
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48 <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 detail' />
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49 <conditional name="k" >
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50 <param argument="--kw" type="select" label="Filter by keyword" >
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51 <option value="None" selected="True">---</option>
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52 <option value="text">Enter keywords</option>
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53 <option value="file">Choose a file containing keywords</option>
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54 </param>
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55 <when value="None" />
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56 <when value="text" >
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57 <param name="txt" type="text" label="Enter keywords or a file containing keywords to be removed" >
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58 <sanitizer>
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59 <valid initial="string.printable">
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60 <remove value="&apos;"/>
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61 </valid>
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62 <mapping initial="none">
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63 <add source="&apos;" target="__sq__"/>
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64 </mapping>
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65 </sanitizer>
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66 </param>
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67 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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68 </when>
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69 <when value="file" >
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70 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
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71 <param name="ncol" type="text" value="c1" label="Please specify the column on which to apply this filter" help='For example, fill in "c1" if the keyword you want to filter out is expected in the first column' />
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72 </when>
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73 </conditional>
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74 </repeat>
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75
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76 <repeat name="value" title="Filter by value" >
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77 <conditional name="v" >
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78 <param argument="--val" type="select" label="Filter by value" >
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79 <option value="None">---</option>
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80 <option value="Equal">=</option>
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81 <option value="Higher">&gt;</option>
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82 <option value="Equal or higher">&gt;=</option>
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83 <option value="Lower">&lt;</option>
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84 <option value="Equal or lower">&lt;=</option>
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85 </param>
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86 <when value="None" >
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87 </when>
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88 <when value="Equal" >
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89 <param name="equal" type="float" value="" label="Value" />
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90 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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91 </when>
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92 <when value="Higher" >
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93 <param type="float" name="higher" value="" label="Value" />
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94 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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95 </when>
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96 <when value="Equal or higher" >
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97 <param type="float" name="equal_higher" value="" label="Value" />
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98 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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99 </when>
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100 <when value="Lower" >
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101 <param type="float" name="lower" value="" label="Value" />
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102 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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103 </when>
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104 <when value="Equal or lower" >
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105 <param type="float" name="equal_lower" value="" label="Value" />
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106 <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
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107 </when>
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108 </conditional>
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109 </repeat>
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110
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111 </inputs>
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112 <outputs>
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113 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
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114 <data name="trash_file" format="tabular" label="Removed proteins from input file" />
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115 </outputs>
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116 <tests>
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117 <test>
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118 <param name="input1" value="UnipIDs.txt" />
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119 <param name="header" value="false" />
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120 <repeat name="keyword">
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121 <param name="match" value="false" />
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122 <conditional name="k">
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123 <param name="kw" value="text" />
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124 <param name="txt" value="A" />
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125 <param name="ncol" value="c3" />
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126 </conditional>
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127 </repeat>
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128 <repeat name="value">
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129 <conditional name="v">
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130 <param name="val" value="Equal or higher"/>
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131 <param name="equal_higher" value="1.0" />
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132 <param name="ncol" value="c2" />
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133 </conditional>
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134 </repeat>
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135 <output name="output1" file="filter_keywords_values_output.txt" />
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136 <output name="trash_file" file="filter_keywords_values_removed.txt" />
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137 </test>
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138 </tests>
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139 <help><![CDATA[
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140 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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141
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142 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output**
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143
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144 **Filter the file by keywords**
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145
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146 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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147
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148 - If you choose to fill in the field, the keywords should be separated by ":", for example: A8K2U0:Q5TA79:O43175
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149
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150 - If you choose to upload a file in a text format in which each line is a keyword, for example:
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151
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152 REV
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153
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154 TRYP_PIG
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155
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156 ALDOA_RABBIT
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157
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158 **The line that contains these keywords will be eliminated from input file.**
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159
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160 **Keywords search can be applied by performing either exact match or partial one by using the following option**
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161
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162 - If you choose **Yes**, only the fields that contains exactly the same content will be removed.
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163
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164 - If you choose **No**, all the fields containing the keyword will be removed.
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165
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166 For example:
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167
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168 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
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169
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170 **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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171
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172 **Filter the file by values**
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173
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174 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.).
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175
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176 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option.
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177
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178 **Output**
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179
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180 The tool will produce 2 output files.
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181
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182 * A text file containing the resulting filtered input file.
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183
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184 * A text file containing the rows removed from the input file.
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185
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186 -----
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187
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188 .. class:: infomark
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189
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190 **Authors**
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191
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192 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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193 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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194
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195 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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196
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197 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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198
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199 ]]></help>
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200 <citations>
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201 </citations>
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202 </tool>